[{"publisher":"Bluefors Oy","main_file_link":[{"url":"https://bluefors.com/blog/application-note-qubit-energy-relaxation-statistics-bluefors-quantum-measurement-system/","open_access":"1"}],"article_processing_charge":"No","type":"other_academic_publication","quality_controlled":"1","language":[{"iso":"eng"}],"month":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Simbierowicz, S., Shi, C., Collodo, M., Kirste, M., Hassani, F., Fink, J. M., … Lake, R. (2021). <i>Qubit energy-relaxation statistics in the Bluefors quantum measurement system</i>. Helsinki, Finland: Bluefors Oy.","ieee":"S. Simbierowicz <i>et al.</i>, <i>Qubit energy-relaxation statistics in the Bluefors quantum measurement system</i>. Helsinki, Finland: Bluefors Oy, 2021.","short":"S. Simbierowicz, C. Shi, M. Collodo, M. Kirste, F. Hassani, J.M. Fink, J. Bylander, D. Perez Lozano, R. Lake, Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System, Bluefors Oy, Helsinki, Finland, 2021.","ama":"Simbierowicz S, Shi C, Collodo M, et al. <i>Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System</i>. Helsinki, Finland: Bluefors Oy; 2021.","ista":"Simbierowicz S, Shi C, Collodo M, Kirste M, Hassani F, Fink JM, Bylander J, Perez Lozano D, Lake R. 2021. Qubit energy-relaxation statistics in the Bluefors quantum measurement system, Helsinki, Finland: Bluefors Oy, 8p.","mla":"Simbierowicz, Slawomir, et al. <i>Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System</i>. Bluefors Oy, 2021.","chicago":"Simbierowicz, Slawomir, Chunyan Shi, Michele Collodo, Moritz Kirste, Farid Hassani, Johannes M Fink, Jonas Bylander, Daniel Perez Lozano, and Russell Lake. <i>Qubit Energy-Relaxation Statistics in the Bluefors Quantum Measurement System</i>. Helsinki, Finland: Bluefors Oy, 2021."},"day":"03","department":[{"_id":"JoFi"}],"oa_version":"Published Version","date_created":"2022-01-19T08:41:14Z","date_published":"2021-06-03T00:00:00Z","date_updated":"2022-01-19T09:11:39Z","page":"8","place":"Helsinki, Finland","publication_status":"published","status":"public","_id":"10645","title":"Qubit energy-relaxation statistics in the Bluefors quantum measurement system","oa":1,"author":[{"first_name":"Slawomir","full_name":"Simbierowicz, Slawomir","last_name":"Simbierowicz"},{"first_name":"Chunyan","full_name":"Shi, Chunyan","last_name":"Shi"},{"full_name":"Collodo, Michele","last_name":"Collodo","first_name":"Michele"},{"first_name":"Moritz","last_name":"Kirste","full_name":"Kirste, Moritz"},{"last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"first_name":"Jonas","full_name":"Bylander, Jonas","last_name":"Bylander"},{"last_name":"Perez Lozano","full_name":"Perez Lozano, Daniel","first_name":"Daniel"},{"full_name":"Lake, Russell","last_name":"Lake","first_name":"Russell"}],"keyword":["Application note"],"abstract":[{"lang":"eng","text":"Superconducting qubits have emerged as a highly versatile and useful platform for quantum technological applications [1]. Bluefors and Zurich Instruments have supported the growth of this field from the 2010s onwards by providing well-engineered and reliable measurement infrastructure [2]– [6]. Having a long and stable qubit lifetime is a critical system property. Therefore, considerable effort has already gone into measuring qubit energy-relaxation timescales and their fluctuations, see Refs. [7]–[10] among others. Accurately extracting the statistics of a quantum device requires users to perform time consuming measurements. One measurement challenge is that the detection of the state-dependent\r\nresponse of a superconducting resonator due to a dispersively-coupled qubit requires an inherently low signal level. Consequently, measurements must be performed using a microwave probe that contains only a few microwave photons. Improving the signal-to-noise ratio (SNR) by using near-quantum limited parametric amplifiers as well as the use of optimized signal processing enabled by efficient room temperature instrumentation help to reduce measurement time. An empirical observation for fixed frequency transmons from recent literature is that as the energy-relaxation time 𝑇𝑇1 increases, so do its natural temporal fluctuations [7], [10]. This necessitates many repeated measurements to understand the statistics (see for example, Ref. [10]). In addition, as state-of-the-art qubits increase in lifetime, longer\r\nmeasurement times are expected to obtain accurate statistics. As described below, the scaling of the widths of the qubit energy-relaxation distributions also reveal clues about the origin of the energy-relaxation."}],"alternative_title":["Bluefors Blog"],"year":"2021"},{"intvolume":"        23","publisher":"Elsevier","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"SaSi"},{"_id":"SiHi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000748748500019"]},"date_published":"2021-12-10T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"scopus_import":"1","date_created":"2022-01-23T23:01:28Z","publication":"Molecular Therapy - Methods and Clinical Development","date_updated":"2023-11-16T13:12:03Z","article_type":"original","page":"210-224","oa":1,"year":"2021","file":[{"creator":"cchlebak","file_size":4794147,"relation":"main_file","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","content_type":"application/pdf","checksum":"77dc540e8011c5475031bdf6ccef20a6","access_level":"open_access","date_updated":"2022-01-24T07:43:09Z","success":1,"date_created":"2022-01-24T07:43:09Z","file_id":"10657"}],"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"},"has_accepted_license":"1","article_processing_charge":"Yes","volume":23,"day":"10","citation":{"ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23. Elsevier, pp. 210–224, 2021.","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., &#38; Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. 2021;23:210-224. doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23, Elsevier, 2021, pp. 210–24, doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>.","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>."},"month":"12","ddc":["570"],"file_date_updated":"2022-01-24T07:43:09Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","publication_identifier":{"eissn":["2329-0501"]},"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","publication_status":"published","status":"public","ec_funded":1,"author":[{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","full_name":"Maes, Margaret E","last_name":"Maes","orcid":"0000-0001-9642-1085"},{"first_name":"Gabriele M.","full_name":"Wögenstein, Gabriele M.","last_name":"Wögenstein"},{"last_name":"Colombo","full_name":"Colombo, Gloria","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902"},{"last_name":"Casado Polanco","full_name":"Casado Polanco, Raquel","first_name":"Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","orcid":"0000-0001-8293-4568"},{"last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"}],"title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","_id":"10655","abstract":[{"text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n","lang":"eng"}],"doi":"10.1016/j.omtm.2021.09.006"},{"date_published":"2021-04-15T00:00:00Z","external_id":{"arxiv":["2104.06966"]},"date_created":"2022-09-09T10:42:51Z","oa_version":"Preprint","citation":{"chicago":"Shute, Alec L. “Sums of Four Squareful Numbers.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.06966\">https://doi.org/10.48550/arXiv.2104.06966</a>.","mla":"Shute, Alec L. “Sums of Four Squareful Numbers.” <i>ArXiv</i>, 2104.06966, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.06966\">10.48550/arXiv.2104.06966</a>.","apa":"Shute, A. L. (n.d.). Sums of four squareful numbers. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.06966\">https://doi.org/10.48550/arXiv.2104.06966</a>","ieee":"A. L. Shute, “Sums of four squareful numbers,” <i>arXiv</i>. .","ama":"Shute AL. Sums of four squareful numbers. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.06966\">10.48550/arXiv.2104.06966</a>","ista":"Shute AL. Sums of four squareful numbers. arXiv, 2104.06966.","short":"A.L. Shute, ArXiv (n.d.)."},"department":[{"_id":"TiBr"}],"day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","article_processing_charge":"No","type":"preprint","language":[{"iso":"eng"}],"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.06966"}],"abstract":[{"lang":"eng","text":"We find an asymptotic formula for the number of primitive vectors $(z_1,\\ldots,z_4)\\in (\\mathbb{Z}_{\\neq 0})^4$ such that $z_1,\\ldots, z_4$ are all squareful and bounded by $B$, and $z_1+\\cdots + z_4 = 0$. Our result agrees in the power of $B$ and $\\log B$ with the Campana-Manin conjecture of Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado."}],"year":"2021","doi":"10.48550/arXiv.2104.06966","title":"Sums of four squareful numbers","oa":1,"author":[{"first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","last_name":"Shute","full_name":"Shute, Alec L","orcid":"0000-0002-1812-2810"}],"_id":"12076","related_material":{"record":[{"id":"12072","relation":"dissertation_contains","status":"public"}]},"publication_status":"submitted","status":"public","article_number":"2104.06966","publication":"arXiv","date_updated":"2023-02-21T16:37:30Z"},{"external_id":{"arxiv":["2104.14946"]},"date_published":"2021-04-30T00:00:00Z","date_created":"2022-09-09T10:43:17Z","oa_version":"Preprint","citation":{"ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>","short":"A.L. Shute, ArXiv (n.d.).","ista":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. arXiv, 2104.14946.","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>arXiv</i>. .","apa":"Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, 2104.14946, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>.","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>."},"day":"30","department":[{"_id":"TiBr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","article_processing_charge":"No","language":[{"iso":"eng"}],"type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.14946"}],"arxiv":1,"abstract":[{"text":"We compare the Manin-type conjecture for Campana points recently formulated\r\nby Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$, where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that the two predicted leading constants do not agree, and we discuss whether thin sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding to squareful values of binary quadratic forms.","lang":"eng"}],"year":"2021","doi":"10.48550/arXiv.2104.14946","oa":1,"title":"On the leading constant in the Manin-type conjecture for Campana points","author":[{"orcid":"0000-0002-1812-2810","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","full_name":"Shute, Alec L","last_name":"Shute"}],"_id":"12077","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12072"}]},"status":"public","acknowledgement":"The author would like to thank Damaris Schindler and Florian Wilsch for their helpful comments on the heights and Tamagawa measures used in Section 3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable feedback on an earlier version of this paper, and Tim Browning for many useful comments and discussions during the development of this work. The author is also grateful to the anonymous referee for providing many valuable comments and suggestions that improved the quality of the paper.","publication_status":"submitted","article_number":"2104.14946","publication":"arXiv","date_updated":"2023-02-21T16:37:30Z"},{"oa_version":"None","month":"08","pmid":1,"citation":{"mla":"Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>, vol. 72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>.","chicago":"Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>.","apa":"Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou, B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>","ieee":"P. Ding <i>et al.</i>, “Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors,” <i>Journal of Experimental Botany</i>, vol. 72, no. 22. Oxford University Press, pp. 7927–7941, 2021.","ama":"Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. 2021;72(22):7927-7941. doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>","ista":"Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 72(22), 7927–7941.","short":"P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M. Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones, Journal of Experimental Botany 72 (2021) 7927–7941."},"day":"13","article_processing_charge":"No","volume":72,"doi":"10.1093/jxb/erab373","abstract":[{"text":"Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.","lang":"eng"}],"issue":"22","_id":"12186","title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","author":[{"first_name":"Pingtao","last_name":"Ding","full_name":"Ding, Pingtao"},{"first_name":"Toshiyuki","full_name":"Sakai, Toshiyuki","last_name":"Sakai"},{"first_name":"Ram","full_name":"Krishna Shrestha, Ram","last_name":"Krishna Shrestha"},{"full_name":"Manosalva Perez, Nicolas","last_name":"Manosalva Perez","first_name":"Nicolas"},{"last_name":"Guo","full_name":"Guo, Wenbin","first_name":"Wenbin"},{"first_name":"Bruno Pok Man","last_name":"Ngou","full_name":"Ngou, Bruno Pok Man"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"full_name":"Liu, Chang","last_name":"Liu","first_name":"Chang"},{"orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Zhang","full_name":"Zhang, Runxuan","first_name":"Runxuan"},{"first_name":"Klaas","full_name":"Vandepoele, Klaas","last_name":"Vandepoele"},{"first_name":"Dan","full_name":"MacLean, Dan","last_name":"MacLean"},{"full_name":"Jones, Jonathan D G","last_name":"Jones","first_name":"Jonathan D G"}],"acknowledgement":"We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by the Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). ","publication_status":"published","status":"public","publication_identifier":{"issn":["0022-0957","1460-2431"]},"date_created":"2023-01-16T09:14:35Z","scopus_import":"1","date_published":"2021-08-13T00:00:00Z","extern":"1","external_id":{"pmid":["34387350"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"XiFe"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Oxford University Press","intvolume":"        72","keyword":["Plant Science","Physiology"],"year":"2021","page":"7927-7941","article_type":"original","date_updated":"2023-05-08T11:01:18Z","publication":"Journal of Experimental Botany"},{"pmid":1,"month":"07","day":"02","citation":{"ama":"Long J, Walker J, She W, et al. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>","ista":"Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 373(6550).","short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021).","apa":"Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X. (2021). Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science (AAAS). <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>","ieee":"J. Long <i>et al.</i>, “Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science (AAAS), 2021.","mla":"Long, Jincheng, et al. “Nurse Cell--Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>, vol. 373, no. 6550, American Association for the Advancement of Science (AAAS), 2021, doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>.","chicago":"Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell--Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science (AAAS), 2021. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>."},"oa_version":"None","article_processing_charge":"No","volume":373,"_id":"12187","author":[{"first_name":"Jincheng","last_name":"Long","full_name":"Long, Jincheng"},{"last_name":"Walker","full_name":"Walker, James","first_name":"James"},{"full_name":"She, Wenjing","last_name":"She","first_name":"Wenjing"},{"first_name":"Billy","full_name":"Aldridge, Billy","last_name":"Aldridge"},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"last_name":"Deans","full_name":"Deans, Samuel","first_name":"Samuel"},{"first_name":"Martin","last_name":"Vickers","full_name":"Vickers, Martin"},{"full_name":"Feng, Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"}],"title":"Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis","doi":"10.1126/science.abh0556","issue":"6550","abstract":[{"text":"Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations.","lang":"eng"}],"publication_identifier":{"issn":["0036-8075","1095-9203"]},"publication_status":"published","acknowledgement":"We thank the John Innes Centre Bioimaging Facility (S. Lopez, E. Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience Institute Partnership Computing Infrastructure for Science Group for high-performance computing resources. Funding: This work was funded by a European Research Council Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship (BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data. Competing interests: The authors declare no competing interests. Data and material availability: All sequencing data have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE161625. Accession nos. of published datasets used in this study are listed in table S6. Published software used in this study include Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167), Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452), and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore and https://github.com/broadinstitute/picard, respectively. All remaining data are in the main paper or the supplementary materials.","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"XiFe"}],"scopus_import":"1","date_created":"2023-01-16T09:15:14Z","extern":"1","external_id":{"pmid":["34210850"]},"date_published":"2021-07-02T00:00:00Z","intvolume":"       373","publisher":"American Association for the Advancement of Science (AAAS)","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","keyword":["Multidisciplinary"],"year":"2021","date_updated":"2023-05-08T10:56:39Z","publication":"Science","article_type":"original"},{"publication":"27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems","date_updated":"2025-07-14T09:09:51Z","page":"20-37","oa":1,"year":"2021","alternative_title":["LNCS"],"intvolume":"     12651","publisher":"Springer Nature","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2101.02594"]},"date_published":"2021-03-21T00:00:00Z","scopus_import":"1","date_created":"2023-03-26T22:01:09Z","publication_identifier":{"isbn":["9783030720155"],"issn":["0302-9743"],"eissn":["1611-3349"]},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"acknowledgement":"We thank anonymous reviewers for valuable inputs. This work is supported in part by NSF grant 2030859 to the CRA for the CIFellows Project, NSF grants IIS-1527668, CCF-1704883, IIS-1830549, the ERC CoG 863818 (ForM-SMArt), and an award from the Maryland Procurement Office.","publication_status":"published","status":"public","ec_funded":1,"author":[{"first_name":"Suguman","last_name":"Bansal","full_name":"Bansal, Suguman"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Vardi","full_name":"Vardi, Moshe Y.","first_name":"Moshe Y."}],"title":"On satisficing in quantitative games","_id":"12767","abstract":[{"lang":"eng","text":"Several problems in planning and reactive synthesis can be reduced to the analysis of two-player quantitative graph games. Optimization is one form of analysis. We argue that in many cases it may be better to replace the optimization problem with the satisficing problem, where instead of searching for optimal solutions, the goal is to search for solutions that adhere to a given threshold bound.\r\nThis work defines and investigates the satisficing problem on a two-player graph game with the discounted-sum cost model. We show that while the satisficing problem can be solved using numerical methods just like the optimization problem, this approach does not render compelling benefits over optimization. When the discount factor is, however, an integer, we present another approach to satisficing, which is purely based on automata methods. We show that this approach is algorithmically more performant – both theoretically and empirically – and demonstrates the broader applicability of satisficing over optimization."}],"doi":"10.1007/978-3-030-72016-2","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"},"file":[{"date_created":"2023-03-28T11:00:33Z","file_id":"12777","date_updated":"2023-03-28T11:00:33Z","success":1,"content_type":"application/pdf","checksum":"b020b78b23587ce7610b1aafb4e63438","access_level":"open_access","creator":"dernst","file_size":747418,"relation":"main_file","file_name":"2021_LNCS_Bansal.pdf"}],"arxiv":1,"has_accepted_license":"1","article_processing_charge":"No","volume":12651,"day":"21","citation":{"ieee":"S. Bansal, K. Chatterjee, and M. Y. Vardi, “On satisficing in quantitative games,” in <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, Luxembourg City, Luxembourg, 2021, vol. 12651, pp. 20–37.","apa":"Bansal, S., Chatterjee, K., &#38; Vardi, M. Y. (2021). On satisficing in quantitative games. In <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 12651, pp. 20–37). Luxembourg City, Luxembourg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-72016-2\">https://doi.org/10.1007/978-3-030-72016-2</a>","ista":"Bansal S, Chatterjee K, Vardi MY. 2021. On satisficing in quantitative games. 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 12651, 20–37.","short":"S. Bansal, K. Chatterjee, M.Y. Vardi, in:, 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2021, pp. 20–37.","ama":"Bansal S, Chatterjee K, Vardi MY. On satisficing in quantitative games. In: <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 12651. Springer Nature; 2021:20-37. doi:<a href=\"https://doi.org/10.1007/978-3-030-72016-2\">10.1007/978-3-030-72016-2</a>","chicago":"Bansal, Suguman, Krishnendu Chatterjee, and Moshe Y. Vardi. “On Satisficing in Quantitative Games.” In <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 12651:20–37. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-72016-2\">https://doi.org/10.1007/978-3-030-72016-2</a>.","mla":"Bansal, Suguman, et al. “On Satisficing in Quantitative Games.” <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 12651, Springer Nature, 2021, pp. 20–37, doi:<a href=\"https://doi.org/10.1007/978-3-030-72016-2\">10.1007/978-3-030-72016-2</a>."},"file_date_updated":"2023-03-28T11:00:33Z","ddc":["000"],"month":"03","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Luxembourg City, Luxembourg","start_date":"2021-03-27","end_date":"2021-04-01"},"oa_version":"Published Version"},{"date_updated":"2023-05-16T07:43:54Z","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]},"publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","page":"5","publication_status":"published","status":"public","_id":"12909","oa":1,"title":"Managing software on a heterogenous HPC cluster","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"full_name":"Elefante, Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"id":"77129392-B450-11EA-8745-D4653DDC885E","first_name":"Andrei","full_name":"Hornoiu, Andrei","last_name":"Hornoiu"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer"}],"doi":"10.3359/2021hpc","year":"2021","publisher":"University of Ljubljana","file":[{"file_id":"12971","date_created":"2023-05-16T07:36:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"ba73f85858fb9d5737ebc7724646dd45","success":1,"date_updated":"2023-05-16T07:36:34Z","file_name":"2021_ASHPC_Schloegl.pdf","creator":"dernst","file_size":422761,"relation":"main_file"}],"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"conference_abstract","has_accepted_license":"1","month":"06","file_date_updated":"2023-05-16T07:36:34Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, University of Ljubljana, 2021, p. 5, doi:<a href=\"https://doi.org/10.3359/2021hpc\">10.3359/2021hpc</a>.","chicago":"Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer. “Managing Software on a Heterogenous HPC Cluster.” In <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, 5. University of Ljubljana, 2021. <a href=\"https://doi.org/10.3359/2021hpc\">https://doi.org/10.3359/2021hpc</a>.","ieee":"A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software on a heterogenous HPC cluster,” in <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, Virtual, 2021, p. 5.","apa":"Schlögl, A., Elefante, S., Hornoiu, A., &#38; Stadlbauer, S. (2021). Managing software on a heterogenous HPC cluster. In <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i> (p. 5). Virtual: University of Ljubljana. <a href=\"https://doi.org/10.3359/2021hpc\">https://doi.org/10.3359/2021hpc</a>","ama":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous HPC cluster. In: <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>. University of Ljubljana; 2021:5. doi:<a href=\"https://doi.org/10.3359/2021hpc\">10.3359/2021hpc</a>","ista":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC - Austrian-Slovenian HPC Meeting, 5.","short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5."},"day":"02","department":[{"_id":"ScienComp"}],"oa_version":"Published Version","date_created":"2023-05-05T13:17:36Z","conference":{"name":"ASHPC - Austrian-Slovenian HPC Meeting","start_date":"2021-05-31","location":"Virtual","end_date":"2021-06-02"},"date_published":"2021-06-02T00:00:00Z"},{"_id":"12987","author":[{"full_name":"Koch, Eva","last_name":"Koch","first_name":"Eva"},{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","oa":1,"doi":"10.5061/DRYAD.ZGMSBCCB4","year":"2021","abstract":[{"lang":"eng","text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome."}],"date_updated":"2023-08-08T13:34:07Z","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9394"}]},"month":"04","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"day":"10","citation":{"mla":"Koch, Eva, et al. <i>Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis</i>. Dryad, 2021, doi:<a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">10.5061/DRYAD.ZGMSBCCB4</a>.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. <a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">https://doi.org/10.5061/DRYAD.ZGMSBCCB4</a>.","ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">10.5061/DRYAD.ZGMSBCCB4</a>.","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:<a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">10.5061/DRYAD.ZGMSBCCB4</a>","ieee":"E. Koch <i>et al.</i>, “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">https://doi.org/10.5061/DRYAD.ZGMSBCCB4</a>"},"oa_version":"Published Version","date_created":"2023-05-16T12:34:09Z","date_published":"2021-04-10T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.zgmsbccb4","open_access":"1"}],"publisher":"Dryad","type":"research_data_reference","article_processing_charge":"No","has_accepted_license":"1"},{"file":[{"date_updated":"2022-07-29T22:30:05Z","access_level":"closed","checksum":"77436be3563a90435024307b1b5ee7e8","content_type":"application/x-zip-compressed","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","creator":"nagrawal","relation":"source_file","file_size":22859658,"file_id":"9744","date_created":"2021-07-28T13:32:02Z","embargo_to":"open_access"},{"file_id":"9745","date_created":"2021-07-28T13:32:05Z","access_level":"open_access","content_type":"application/pdf","checksum":"72a891d7daba85445c29b868c22575ed","date_updated":"2022-07-29T22:30:05Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","creator":"nagrawal","file_size":18658048,"relation":"main_file","embargo":"2022-07-28"}],"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"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","month":"07","ddc":["532"],"file_date_updated":"2022-07-29T22:30:05Z","day":"29","citation":{"mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>"},"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","_id":"9728","author":[{"last_name":"Agrawal","full_name":"Agrawal, Nishchal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"}],"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","supervisor":[{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"doi":"10.15479/at:ista:9728","abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"date_created":"2021-07-27T13:40:30Z","date_published":"2021-07-29T00:00:00Z","date_updated":"2024-02-28T13:14:39Z","page":"118","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6189"}]},"oa":1,"keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"year":"2021","alternative_title":["ISTA Thesis"]},{"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nd/4.0/","file_date_updated":"2022-03-10T12:13:57Z","month":"08","ddc":["515","519","539"],"citation":{"chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9733\">https://doi.org/10.15479/at:ista:9733</a>.","mla":"Feliciangeli, Dario. <i>The Polaron at Strong Coupling</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9733\">10.15479/at:ista:9733</a>.","apa":"Feliciangeli, D. (2021). <i>The polaron at strong coupling</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9733\">https://doi.org/10.15479/at:ista:9733</a>","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9733\">10.15479/at:ista:9733</a>"},"day":"20","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"Thesis_FeliciangeliA.pdf","file_size":1958710,"creator":"dfelicia","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"e88bb8ca43948abe060eb2d2fa719881","date_updated":"2021-09-06T09:28:56Z","file_id":"9944","date_created":"2021-08-19T14:03:48Z"},{"file_id":"9945","date_created":"2021-08-19T14:06:35Z","date_updated":"2022-03-10T12:13:57Z","access_level":"closed","content_type":"application/octet-stream","checksum":"72810843abee83705853505b3f8348aa","file_name":"thesis.7z","relation":"source_file","file_size":3771669,"creator":"dfelicia"}],"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"degree_awarded":"PhD","doi":"10.15479/at:ista:9733","abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"_id":"9733","title":"The polaron at strong coupling","supervisor":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0002-0845-1338","last_name":"Maas","full_name":"Maas, Jan","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"author":[{"orcid":"0000-0003-0754-8530","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario"}],"ec_funded":1,"status":"public","publication_status":"published","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"publication_identifier":{"issn":["2663-337X"]},"date_created":"2021-07-27T15:48:30Z","date_published":"2021-08-20T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2021","oa":1,"page":"180","related_material":{"record":[{"id":"9787","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9792"},{"relation":"part_of_dissertation","status":"public","id":"9225"},{"relation":"part_of_dissertation","status":"public","id":"9781"},{"relation":"part_of_dissertation","status":"public","id":"9791"}]},"date_updated":"2024-03-06T12:30:44Z"},{"abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}],"doi":"10.7554/elife.68876","author":[{"first_name":"Aditi","full_name":"Batra, Aditi","last_name":"Batra"},{"orcid":"0000-0001-9480-5261","first_name":"Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","last_name":"Römhild","full_name":"Römhild, Roderich"},{"last_name":"Rousseau","full_name":"Rousseau, Emilie","first_name":"Emilie"},{"first_name":"Sören","last_name":"Franzenburg","full_name":"Franzenburg, Sören"},{"first_name":"Stefan","full_name":"Niemann, Stefan","last_name":"Niemann"},{"last_name":"Schulenburg","full_name":"Schulenburg, Hinrich","first_name":"Hinrich"}],"title":"High potency of sequential therapy with only beta-lactam antibiotics","_id":"9746","acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","publication_status":"published","status":"public","publication_identifier":{"eissn":["2050-084X"]},"oa_version":"Published Version","day":"28","citation":{"ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., &#38; Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>, vol. 10, e68876, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>.","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>."},"month":"07","pmid":1,"volume":10,"article_processing_charge":"No","year":"2021","oa":1,"article_type":"original","article_number":"e68876","publication":"eLife","date_updated":"2023-08-11T10:26:29Z","date_published":"2021-07-28T00:00:00Z","external_id":{"isi":["000692027800001"],"pmid":["34318749"]},"scopus_import":"1","date_created":"2021-07-28T13:36:57Z","department":[{"_id":"CaGu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        10","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"publisher":"eLife Sciences Publications"},{"page":"267-283","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}]},"date_updated":"2024-03-25T23:30:16Z","publication":" Receptor and Ion Channel Detection in the Brain","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"alternative_title":["Neuromethods"],"year":"2021","quality_controlled":"1","language":[{"iso":"eng"}],"type":"book_chapter","publisher":"Humana","intvolume":"       169","series_title":"Neuromethods","date_created":"2021-07-30T09:34:56Z","date_published":"2021-07-27T00:00:00Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"place":"New York","ec_funded":1,"publication_status":"published","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.).","status":"public","project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eisbn":["9781071615225"],"isbn":["9781071615218"]},"doi":"10.1007/978-1-0716-1522-5_19","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."}],"_id":"9756","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","author":[{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"last_name":"Kleindienst","full_name":"Kleindienst, David","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7429-7896","last_name":"Harada","full_name":"Harada, Harumi","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"article_processing_charge":"No","volume":169,"has_accepted_license":"1","oa_version":"None","month":"07","ddc":["573"],"citation":{"short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:,  Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.","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.","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; 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>","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. <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>","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, 2021, pp. 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, 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>.","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, 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>."},"day":"27"},{"citation":{"ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. 2021;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” <i>PLoS Computational Biology</i>, vol. 17, no. 7. Public Library of Science, 2021.","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., &#38; Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>.","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>."},"day":"15","ddc":["613"],"pmid":1,"month":"07","file_date_updated":"2021-08-05T12:06:49Z","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"},"file":[{"file_name":"2021_PlosCompBio_Bartlett.pdf","relation":"main_file","creator":"cchlebak","file_size":693633,"access_level":"open_access","content_type":"application/pdf","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","date_updated":"2021-08-05T12:06:49Z","file_id":"9771","date_created":"2021-08-05T12:06:49Z"}],"has_accepted_license":"1","volume":17,"article_processing_charge":"Yes","title":"Ten simple rules to improve academic work- life balance","author":[{"full_name":"Bartlett, Michael John","last_name":"Bartlett","first_name":"Michael John"},{"orcid":"0000-0001-5809-9566","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","full_name":"Arslan, Feyza N"},{"first_name":"Adriana","full_name":"Bankston, Adriana","last_name":"Bankston"},{"last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz"}],"_id":"9759","issue":"7","doi":"10.1371/journal.pcbi.1009124","publication_identifier":{"eissn":["15537358"],"issn":["1553734X"]},"status":"public","publication_status":"published","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","department":[{"_id":"CaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"date_published":"2021-07-15T00:00:00Z","date_created":"2021-08-01T22:01:21Z","scopus_import":"1","publisher":"Public Library of Science","intvolume":"        17","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2021","publication":"PLoS Computational Biology","date_updated":"2023-08-10T14:16:46Z","article_number":"e1009124","article_type":"letter_note"},{"publication_identifier":{"eissn":["2521-327X"]},"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"publication_status":"published","status":"public","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).","ec_funded":1,"title":"Quantum annealing initialization of the quantum approximate optimization algorithm","author":[{"orcid":"0000-0001-5400-8508","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","full_name":"Sack, Stefan"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"_id":"9760","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"}],"doi":"10.22331/Q-2021-07-01-491","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"},"file":[{"file_id":"9774","date_created":"2021-08-06T06:44:31Z","access_level":"open_access","content_type":"application/pdf","checksum":"9706c2bb8e748e9b5b138381995a7f6f","date_updated":"2021-08-06T06:44:31Z","file_name":"2021_Quantum_Sack.pdf","relation":"main_file","creator":"cchlebak","file_size":2312482}],"arxiv":1,"has_accepted_license":"1","article_processing_charge":"Yes","volume":5,"citation":{"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>.","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>.","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","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>","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","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>"},"day":"01","file_date_updated":"2021-08-06T06:44:31Z","ddc":["530"],"month":"07","oa_version":"Published Version","publication":"Quantum","date_updated":"2023-12-13T14:47:25Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14622"}]},"article_number":"491","article_type":"original","oa":1,"year":"2021","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","intvolume":"         5","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-07-01T00:00:00Z","external_id":{"arxiv":["2101.05742"],"isi":["000669830600001"]},"date_created":"2021-08-01T22:01:21Z","scopus_import":"1"},{"intvolume":"        10","publisher":"MDPI","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SaSi"}],"scopus_import":"1","date_created":"2021-08-01T22:01:22Z","external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"date_published":"2021-06-25T00:00:00Z","date_updated":"2023-08-10T14:14:53Z","publication":"Cells","article_type":"original","article_number":"1593","oa":1,"year":"2021","file":[{"date_created":"2021-08-04T14:01:30Z","file_id":"9768","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-08-04T14:01:30Z","success":1,"file_size":4555611,"creator":"cziletti","relation":"main_file","file_name":"2021_Cells_Muench.pdf"}],"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"},"article_processing_charge":"Yes","volume":10,"has_accepted_license":"1","month":"06","file_date_updated":"2021-08-04T14:01:30Z","pmid":1,"ddc":["570"],"day":"25","citation":{"apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., &#38; Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” <i>Cells</i>, vol. 10, no. 7. MDPI, 2021.","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. 2021;10(7). doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>, vol. 10, no. 7, 1593, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>.","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>."},"oa_version":"Published Version","publication_identifier":{"eissn":["20734409"]},"acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","publication_status":"published","status":"public","_id":"9761","author":[{"full_name":"Muench, Nicole A.","last_name":"Muench","first_name":"Nicole A."},{"last_name":"Patel","full_name":"Patel, Sonia","first_name":"Sonia"},{"full_name":"Maes, Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085"},{"full_name":"Donahue, Ryan J.","last_name":"Donahue","first_name":"Ryan J."},{"first_name":"Akihiro","last_name":"Ikeda","full_name":"Ikeda, Akihiro"},{"first_name":"Robert W.","last_name":"Nickells","full_name":"Nickells, Robert W."}],"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","doi":"10.3390/cells10071593","issue":"7","abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}]},{"publisher":"SciPost","intvolume":"        11","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"date_created":"2021-08-04T15:00:55Z","scopus_import":"1","date_published":"2021-07-13T00:00:00Z","external_id":{"arxiv":["2101.10958"],"isi":["000680039500013"]},"date_updated":"2023-08-11T10:25:44Z","publication":"SciPost Physics","article_number":"008","article_type":"original","oa":1,"year":"2021","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"},"file":[{"success":1,"date_updated":"2021-08-10T11:44:59Z","access_level":"open_access","checksum":"eaa847346b1a023d97bbb291779610ed","content_type":"application/pdf","file_name":"2021_SciPostPhysics_Brauneis.pdf","relation":"main_file","creator":"asandaue","file_size":1085300,"file_id":"9875","date_created":"2021-08-10T11:44:59Z"}],"arxiv":1,"volume":11,"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2021-08-10T11:44:59Z","ddc":["530"],"month":"07","citation":{"chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>. SciPost, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>.","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>, vol. 11, no. 1, 008, SciPost, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” <i>SciPost Physics</i>, vol. 11, no. 1. SciPost, 2021.","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., &#38; Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. SciPost. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>"},"day":"13","oa_version":"Published Version","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["2542-4653"]},"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","_id":"9769","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","author":[{"first_name":"Fabian","full_name":"Brauneis, Fabian","last_name":"Brauneis"},{"last_name":"Hammer","full_name":"Hammer, Hans-Werner","first_name":"Hans-Werner"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.21468/scipostphys.11.1.008","abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}],"issue":"1"},{"year":"2021","oa":1,"article_type":"original","article_number":"024430","publication":"Physical Review B","date_updated":"2023-08-10T14:27:07Z","external_id":{"arxiv":["2101.05173"],"isi":["000678780800003"]},"date_published":"2021-07-01T00:00:00Z","scopus_import":"1","date_created":"2021-08-04T15:05:32Z","department":[{"_id":"MiLe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/2101.05173","open_access":"1"}],"intvolume":"       104","publisher":"American Physical Society","issue":"2","abstract":[{"text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data.","lang":"eng"}],"doi":"10.1103/physrevb.104.024430","author":[{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"},{"first_name":"Hen","full_name":"Alpern, Hen","last_name":"Alpern"},{"first_name":"Yossi","full_name":"Paltiel, Yossi","last_name":"Paltiel"},{"last_name":"Millo","full_name":"Millo, Oded","first_name":"Oded"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"}],"title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","_id":"9770","status":"public","publication_status":"published","acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","ec_funded":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"oa_version":"Preprint","day":"01","citation":{"ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. 2021;104(2). doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430.","short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., &#38; Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” <i>Physical Review B</i>, vol. 104, no. 2. American Physical Society, 2021.","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>.","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>."},"month":"07","volume":104,"article_processing_charge":"No","arxiv":1},{"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"intvolume":"        12","publisher":"Springer","scopus_import":"1","acknowledged_ssus":[{"_id":"SSU"}],"date_created":"2021-08-06T07:22:55Z","date_published":"2021-05-18T00:00:00Z","external_id":{"isi":["000655481800014"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"PeJo"}],"article_type":"original","article_number":"2912","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/"}]},"date_updated":"2023-08-10T14:16:16Z","publication":"Nature Communications","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"year":"2021","oa":1,"volume":12,"article_processing_charge":"No","has_accepted_license":"1","file":[{"creator":"kschuh","relation":"main_file","file_size":3108845,"file_name":"2021_NatureCommunications_Vandael.pdf","checksum":"6036a8cdae95e1707c2a04d54e325ff4","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-12-17T11:34:50Z","success":1,"date_created":"2021-12-17T11:34:50Z","file_id":"10563"}],"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","file_date_updated":"2021-12-17T11:34:50Z","ddc":["570"],"month":"05","day":"18","citation":{"ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>."},"ec_funded":1,"acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","publication_status":"published","status":"public","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-021-23153-5","issue":"1","abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses."}],"_id":"9778","author":[{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","first_name":"Yuji","full_name":"Okamoto, Yuji","last_name":"Okamoto","orcid":"0000-0003-0408-6094"},{"full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses"},{"abstract":[{"lang":"eng","text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging."}],"_id":"9787","title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"ec_funded":1,"publication_status":"submitted","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.1.\r\n","status":"public","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"oa_version":"Preprint","month":"02","ddc":["510"],"citation":{"mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>ArXiv</i>, 2101.12566.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>ArXiv</i>, n.d.","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” <i>arXiv</i>. .","apa":"Feliciangeli, D., &#38; Seiringer, R. (n.d.). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>arXiv</i>.","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>arXiv</i>.","short":"D. Feliciangeli, R. Seiringer, ArXiv (n.d.).","ista":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. arXiv, 2101.12566."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","arxiv":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"},"year":"2021","oa":1,"article_number":"2101.12566","related_material":{"record":[{"relation":"later_version","status":"public","id":"10224"},{"id":"9733","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-07T13:30:10Z","publication":"arXiv","date_created":"2021-08-06T08:25:57Z","external_id":{"arxiv":["2101.12566"]},"date_published":"2021-02-01T00:00:00Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"type":"preprint","main_file_link":[{"url":"https://arxiv.org/abs/2101.12566","open_access":"1"}]}]