[{"OA_place":"publisher","date_published":"2021-01-01T00:00:00Z","ddc":["005"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","related_material":{"record":[{"status":"public","id":"6490","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6780","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7158"},{"relation":"part_of_dissertation","id":"66","status":"public"},{"relation":"part_of_dissertation","id":"6378","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"311"},{"relation":"part_of_dissertation","status":"public","id":"6175"},{"relation":"part_of_dissertation","status":"public","id":"6340"},{"id":"7014","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6009","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"status":"public","id":"8728","relation":"part_of_dissertation"},{"status":"public","id":"8089","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6380","status":"public"},{"relation":"part_of_dissertation","id":"5977","status":"public"},{"status":"public","id":"6056","relation":"part_of_dissertation"},{"status":"public","id":"639","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1386","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6918"},{"id":"7810","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"949"}]},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"year":"2021","author":[{"first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584"}],"date_updated":"2026-04-16T10:07:18Z","article_processing_charge":"No","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","degree_awarded":"PhD","file":[{"creator":"akafshda","file_size":5251507,"embargo":"2021-12-22","file_id":"8969","checksum":"d1b9db3725aed34dadd81274aeb9426c","date_updated":"2021-12-23T23:30:04Z","relation":"main_file","content_type":"application/pdf","date_created":"2020-12-22T20:08:44Z","file_name":"Thesis-pdfa.pdf","access_level":"open_access"},{"checksum":"1661df7b393e6866d2460eba3c905130","file_size":10636756,"creator":"akafshda","file_id":"8970","date_created":"2020-12-22T20:08:50Z","file_name":"source.zip","access_level":"closed","embargo_to":"open_access","relation":"source_file","date_updated":"2021-03-04T23:30:04Z","content_type":"application/zip"}],"date_created":"2020-12-10T12:17:07Z","publication_identifier":{"issn":["2663-337X"]},"status":"public","alternative_title":["ISTA Thesis"],"month":"01","page":"278","oa":1,"project":[{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8934","title":"Parameterized and algebro-geometric advances in static program analysis","fulldoi":"https://doi.org/10.15479/AT:ISTA:8934","_id":"8934","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","day":"01","citation":{"ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021."},"file_date_updated":"2021-12-23T23:30:04Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"page":"182","oa":1,"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration"}],"doi":"10.15479/at:ista:9962","language":[{"iso":"eng"}],"file":[{"file_id":"9971","file_size":10629190,"creator":"ahansen","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-09-03T22:30:04Z","relation":"source_file","embargo_to":"open_access","file_name":"Thesis_Hansen.docx","access_level":"closed","date_created":"2021-08-30T09:17:39Z"},{"embargo":"2022-09-02","file_id":"9972","file_size":13457469,"creator":"ahansen","checksum":"204fa40321a1c6289b68c473634c4bf3","content_type":"application/pdf","relation":"main_file","date_updated":"2022-09-03T22:30:04Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","date_created":"2021-08-30T09:29:44Z"}],"publication_identifier":{"issn":["2663-337X"]},"date_created":"2021-08-29T12:36:50Z","status":"public","alternative_title":["ISTA Thesis"],"month":"09","day":"02","citation":{"apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria."},"file_date_updated":"2022-09-03T22:30:04Z","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.15479/at:ista:9962","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","_id":"9962","publication_status":"published","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"publisher":"Institute of Science and Technology Austria","date_published":"2021-09-02T00:00:00Z","OA_place":"publisher","ddc":["570"],"corr_author":"1","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","type":"dissertation","related_material":{"record":[{"status":"public","id":"8569","relation":"part_of_dissertation"},{"id":"960","status":"public","relation":"part_of_dissertation"}]},"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"year":"2021","date_updated":"2026-04-08T07:19:09Z","author":[{"full_name":"Hansen, Andi H","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen"}]},{"file_date_updated":"2021-05-31T09:43:09Z","ec_funded":1,"citation":{"short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>, vol. 10, e68274, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>","ieee":"P. Bhandari <i>et al.</i>, “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal C, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","publication_status":"published","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","_id":"9437","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","fulldoi":"https://doi.org/10.7554/ELIFE.68274","article_number":"e68274","language":[{"iso":"eng"}],"doi":"10.7554/ELIFE.68274","article_type":"original","oa":1,"external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"month":"04","file":[{"checksum":"6ebcb79999f889766f7cd79ee134ad28","success":1,"creator":"cziletti","file_size":8174719,"file_id":"9440","date_created":"2021-05-31T09:43:09Z","file_name":"2021_eLife_Bhandari.pdf","access_level":"open_access","relation":"main_file","date_updated":"2021-05-31T09:43:09Z","content_type":"application/pdf"}],"status":"public","date_created":"2021-05-30T22:01:23Z","publication_identifier":{"eissn":["2050-084X"]},"article_processing_charge":"No","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","isi":1,"author":[{"full_name":"Bhandari, Pradeep","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","orcid":"0000-0003-0863-4481"},{"first_name":"David H","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"last_name":"Fernández-Fernández","first_name":"Diego","full_name":"Fernández-Fernández, Diego"},{"last_name":"Fritzius","first_name":"Thorsten","full_name":"Fritzius, Thorsten"},{"first_name":"David","full_name":"Kleindienst, David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hüseyin C","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"last_name":"Gassmann","full_name":"Gassmann, Martin","first_name":"Martin"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"},{"full_name":"Kulik, Akos","first_name":"Akos","last_name":"Kulik"},{"full_name":"Bettler, Bernhard","first_name":"Bernhard","last_name":"Bettler"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"first_name":"Peter","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948"}],"date_updated":"2026-10-09T22:31:07Z","year":"2021","type":"journal_article","scopus_import":"1","related_material":{"record":[{"id":"19271","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"9562","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}]},"department":[{"_id":"RySh"},{"_id":"PeJo"}],"volume":10,"intvolume":"        10","publisher":"eLife Sciences Publications","abstract":[{"text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.","lang":"eng"}],"quality_controlled":"1","ddc":["570"],"has_accepted_license":"1","publication":"eLife","date_published":"2021-04-29T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"corr_author":"1","has_accepted_license":"1","ddc":["570"],"OA_place":"publisher","date_published":"2021-06-01T00:00:00Z","degree_awarded":"PhD","article_processing_charge":"No","year":"2021","date_updated":"2026-07-06T13:11:44Z","author":[{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"9437","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"612"},{"relation":"part_of_dissertation","status":"public","id":"8532"},{"relation":"part_of_dissertation","id":"9756","status":"public"}]},"type":"dissertation","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9562","page":"124","oa":1,"month":"06","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"date_created":"2021-06-17T14:10:47Z","status":"public","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2022-07-02T22:30:04Z","access_level":"open_access","file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z","embargo":"2022-07-01","file_id":"9563","file_size":77299142,"creator":"dkleindienst","checksum":"659df5518db495f679cb1df9e9bd1d94"},{"checksum":"3bcf63a2b19e5b6663be051bea332748","file_size":369804895,"creator":"dkleindienst","file_id":"9564","date_created":"2021-06-17T14:04:30Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_source.zip","date_updated":"2022-07-02T22:30:04Z","relation":"source_file","content_type":"application/zip"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>."},"file_date_updated":"2022-07-02T22:30:04Z","day":"01","oa_version":"Published Version","publication_status":"published","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","fulldoi":"https://doi.org/10.15479/at:ista:9562","_id":"9562"},{"type":"book_chapter","scopus_import":"1","related_material":{"record":[{"status":"public","id":"9562","relation":"dissertation_contains"}]},"department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"volume":169,"place":"New York","year":"2021","author":[{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter"},{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","first_name":"David"},{"first_name":"Harumi","full_name":"Harada, Harumi","last_name":"Harada","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"}],"date_updated":"2026-10-09T22:31:07Z","article_processing_charge":"No","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","date_published":"2021-07-27T00:00:00Z","publication":"Receptor and Ion Channel Detection in the Brain","ddc":["573"],"quality_controlled":"1","corr_author":"1","series_title":"Neuromethods","has_accepted_license":"1","abstract":[{"lang":"eng","text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms."}],"intvolume":"       169","publisher":"Humana Press","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","fulldoi":"https://doi.org/10.1007/978-1-0716-1522-5_19","_id":"9756","publication_status":"published","oa_version":"None","day":"27","citation":{"ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, vol. 169, New York: Humana Press, 2021, pp. 267–283.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., &#38; Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (Vol. 169, pp. 267–283). New York: Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana Press, New York, 2021, pp. 267–283.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, vol. 169, Humana Press, 2021, pp. 267–83, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 169:267–83. Neuromethods. New York: Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Vol 169. Neuromethods. New York: Humana Press; 2021:267-283. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>"},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"date_created":"2021-07-30T09:34:56Z","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"das_tickbox":"1","status":"public","alternative_title":["Neuromethods"],"month":"07","page":"267-283","project":[{"grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1007/978-1-0716-1522-5_19","language":[{"iso":"eng"}]},{"department":[{"_id":"BjHo"}],"related_material":{"record":[{"id":"19906","status":"public","relation":"dissertation_contains"}]},"volume":118,"type":"journal_article","scopus_import":"1","date_updated":"2026-10-09T22:31:08Z","author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H","full_name":"Choueiri, George H"},{"first_name":"Jose M","full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sankar","full_name":"Sankar, Sarath","first_name":"Sarath"},{"full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"year":"2021","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"arxiv":1,"acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2021-11-03T00:00:00Z","corr_author":"1","quality_controlled":"1","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"publisher":"National Academy of Sciences","intvolume":"       118","_id":"10299","article_number":"e2102350118","fulldoi":"https://doi.org/10.1073/pnas.2102350118","title":"Experimental observation of the origin and structure of elastoinertial turbulence","oa_version":"Preprint","pmid":1,"publication_status":"published","day":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"citation":{"mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., &#38; Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45. National Academy of Sciences, 2021.","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>.","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(45). doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. 118(45), e2102350118."},"status":"public","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_created":"2021-11-17T13:24:24Z","month":"11","issue":"45","project":[{"call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188","name":"Instabilities in pulsating pipe flow in complex fluids"}],"oa":1,"external_id":{"arxiv":["2103.00023"],"pmid":[" 34732570"],"isi":["000720926900019"]},"language":[{"iso":"eng"}],"article_type":"original","doi":"10.1073/pnas.2102350118"},{"day":"01","ec_funded":1,"file_date_updated":"2021-08-06T06:44:31Z","citation":{"ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>.","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. 2021;5. doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” <i>Quantum</i>, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021.","apa":"Sack, S., &#38; Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9760","fulldoi":"https://doi.org/10.22331/Q-2021-07-01-491","article_number":"491","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","publication_status":"published","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"article_type":"original","language":[{"iso":"eng"}],"doi":"10.22331/Q-2021-07-01-491","file":[{"checksum":"9706c2bb8e748e9b5b138381995a7f6f","file_size":2312482,"creator":"cchlebak","file_id":"9774","date_created":"2021-08-06T06:44:31Z","file_name":"2021_Quantum_Sack.pdf","access_level":"open_access","date_updated":"2021-08-06T06:44:31Z","relation":"main_file","content_type":"application/pdf"}],"status":"public","date_created":"2021-08-01T22:01:21Z","publication_identifier":{"eissn":["2521-327X"]},"month":"07","arxiv":1,"acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","article_processing_charge":"Yes","scopus_import":"1","type":"journal_article","volume":5,"related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"isi":1,"date_updated":"2026-10-09T22:31:14Z","author":[{"last_name":"Sack","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","full_name":"Sack, Stefan"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"year":"2021","abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.","lang":"eng"}],"intvolume":"         5","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","publication":"Quantum","date_published":"2021-07-01T00:00:00Z","quality_controlled":"1","ddc":["530"],"has_accepted_license":"1","corr_author":"1"},{"file":[{"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","file_id":"11352","success":1,"creator":"dernst","file_size":1008594,"access_level":"open_access","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","date_created":"2022-05-06T09:47:18Z","content_type":"application/pdf","date_updated":"2022-05-06T09:47:18Z","relation":"main_file"}],"date_created":"2021-10-21T07:49:12Z","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"das_tickbox":"1","status":"public","issue":"12","month":"06","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"page":"5345-58","oa":1,"project":[{"grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msab178","article_type":"original","fulldoi":"https://doi.org/10.1093/molbev/msab178","title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","_id":"10167","publication_status":"published","pmid":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"19","citation":{"ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press, 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press, pp. 5345–58, 2021."},"file_date_updated":"2022-05-06T09:47:18Z","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-19T00:00:00Z","publication":"Molecular Biology and Evolution","ddc":["610"],"quality_controlled":"1","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"intvolume":"       138","publisher":"Oxford University Press","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","type":"journal_article","volume":138,"department":[{"_id":"BeVi"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19386"}]},"isi":1,"year":"2021","author":[{"first_name":"Marwan N","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"},{"last_name":"Moldovan","orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A.","first_name":"Mikhail A."},{"first_name":"Marion A L","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","last_name":"Picard"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-10-09T22:31:16Z","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","article_processing_charge":"No"}]