[{"title":"Genetic basis of flower colour as a model for adaptive evolution","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2022-04-07T08:19:54Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"author":[{"id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","first_name":"Lenka","last_name":"Matejovicova","full_name":"Matejovicova, Lenka"}],"_id":"11128","publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-04-07T08:11:51Z","page":"112","abstract":[{"lang":"eng","text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline."}],"degree_awarded":"PhD","doi":"10.15479/at:ista:11128","day":"06","date_updated":"2023-06-23T06:26:41Z","year":"2022","citation":{"ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>.","apa":"Matejovicova, L. (2022). <i>Genetic basis of flower colour as a model for adaptive evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","mla":"Matejovicova, Lenka. <i>Genetic Basis of Flower Colour as a Model for Adaptive Evolution</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>."},"ddc":["576","582"],"month":"04","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"date_published":"2022-04-06T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"access_level":"open_access","relation":"main_file","creator":"cchlebak","file_id":"11129","file_size":11906472,"checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","date_created":"2022-04-07T08:11:34Z","file_name":"LenkaPhD_Official_PDFA.pdf","content_type":"application/pdf","date_updated":"2022-04-07T08:11:34Z"},{"creator":"cchlebak","file_id":"11130","access_level":"closed","relation":"source_file","file_name":"LenkaPhD Official_source.zip","content_type":"application/x-zip-compressed","date_updated":"2022-04-07T08:11:51Z","checksum":"99d67040432fd07a225643a212ee8588","file_size":23036766,"date_created":"2022-04-07T08:11:51Z"}]},{"article_number":"2250036","month":"10","oa_version":"Preprint","publication":"Random Matrices: Theory and Applications","keyword":["Discrete Mathematics and Combinatorics","Statistics","Probability and Uncertainty","Statistics and Probability","Algebra and Number Theory"],"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["2010-3263"],"eissn":["2010-3271"]},"type":"journal_article","date_published":"2022-10-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.03906","open_access":"1"}],"intvolume":"        11","title":"On the operator norm of a Hermitian random matrix with correlated entries","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"article_processing_charge":"No","date_created":"2022-04-08T07:11:12Z","publication_status":"published","issue":"4","author":[{"id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","first_name":"Jana","last_name":"Reker","full_name":"Reker, Jana"}],"scopus_import":"1","_id":"11135","article_type":"original","publisher":"World Scientific","quality_controlled":"1","abstract":[{"text":"We consider a correlated NxN Hermitian random matrix with a polynomially decaying metric correlation structure. By calculating the trace of the moments of the matrix and using the summable decay of the cumulants, we show that its operator norm is stochastically dominated by one.","lang":"eng"}],"day":"01","arxiv":1,"doi":"10.1142/s2010326322500368","external_id":{"arxiv":["2103.03906"],"isi":["000848873800001"]},"isi":1,"citation":{"ama":"Reker J. On the operator norm of a Hermitian random matrix with correlated entries. <i>Random Matrices: Theory and Applications</i>. 2022;11(4). doi:<a href=\"https://doi.org/10.1142/s2010326322500368\">10.1142/s2010326322500368</a>","apa":"Reker, J. (2022). On the operator norm of a Hermitian random matrix with correlated entries. <i>Random Matrices: Theory and Applications</i>. World Scientific. <a href=\"https://doi.org/10.1142/s2010326322500368\">https://doi.org/10.1142/s2010326322500368</a>","ieee":"J. Reker, “On the operator norm of a Hermitian random matrix with correlated entries,” <i>Random Matrices: Theory and Applications</i>, vol. 11, no. 4. World Scientific, 2022.","chicago":"Reker, Jana. “On the Operator Norm of a Hermitian Random Matrix with Correlated Entries.” <i>Random Matrices: Theory and Applications</i>. World Scientific, 2022. <a href=\"https://doi.org/10.1142/s2010326322500368\">https://doi.org/10.1142/s2010326322500368</a>.","short":"J. Reker, Random Matrices: Theory and Applications 11 (2022).","mla":"Reker, Jana. “On the Operator Norm of a Hermitian Random Matrix with Correlated Entries.” <i>Random Matrices: Theory and Applications</i>, vol. 11, no. 4, 2250036, World Scientific, 2022, doi:<a href=\"https://doi.org/10.1142/s2010326322500368\">10.1142/s2010326322500368</a>.","ista":"Reker J. 2022. On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. 11(4), 2250036."},"year":"2022","date_updated":"2023-08-03T06:32:22Z","volume":11},{"language":[{"iso":"eng"}],"publication":"Materials Today Energy","oa_version":"None","project":[{"grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"month":"04","article_number":"100985","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2022-04-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["2468-6069"]},"quality_controlled":"1","publisher":"Elsevier","article_type":"original","_id":"11142","scopus_import":"1","author":[{"first_name":"Tao","last_name":"Hong","full_name":"Hong, Tao"},{"first_name":"Changrong","last_name":"Guo","full_name":"Guo, Changrong"},{"last_name":"Wang","first_name":"Dongyang","full_name":"Wang, Dongyang"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"first_name":"Xiang","last_name":"Gao","full_name":"Gao, Xiang"},{"first_name":"Li Dong","last_name":"Zhao","full_name":"Zhao, Li Dong"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"MaIb"}],"date_created":"2022-04-10T22:01:39Z","title":"Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3","intvolume":"        25","volume":25,"acknowledgement":"This work was supported by National Natural Science Foundation of China (52002042), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), 111 Project (B17002) and Lise Meitner Project M 2889-N. This work was also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the high-performance computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM and TEM measurements.","date_updated":"2023-08-03T06:28:16Z","citation":{"ieee":"T. Hong <i>et al.</i>, “Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3,” <i>Materials Today Energy</i>, vol. 25. Elsevier, 2022.","chicago":"Hong, Tao, Changrong Guo, Dongyang Wang, Bingchao Qin, Cheng Chang, Xiang Gao, and Li Dong Zhao. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” <i>Materials Today Energy</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">https://doi.org/10.1016/j.mtener.2022.100985</a>.","apa":"Hong, T., Guo, C., Wang, D., Qin, B., Chang, C., Gao, X., &#38; Zhao, L. D. (2022). Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. <i>Materials Today Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">https://doi.org/10.1016/j.mtener.2022.100985</a>","ama":"Hong T, Guo C, Wang D, et al. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. <i>Materials Today Energy</i>. 2022;25. doi:<a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">10.1016/j.mtener.2022.100985</a>","ista":"Hong T, Guo C, Wang D, Qin B, Chang C, Gao X, Zhao LD. 2022. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials Today Energy. 25, 100985.","short":"T. Hong, C. Guo, D. Wang, B. Qin, C. Chang, X. Gao, L.D. Zhao, Materials Today Energy 25 (2022).","mla":"Hong, Tao, et al. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” <i>Materials Today Energy</i>, vol. 25, 100985, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">10.1016/j.mtener.2022.100985</a>."},"year":"2022","isi":1,"external_id":{"isi":["000798679100010"]},"doi":"10.1016/j.mtener.2022.100985","day":"01","abstract":[{"text":"SnTe is a promising Pb-free thermoelectric (TE) material with high electrical conductivity. We discovered the synergistic effect of Bi2O3 on enhancing the average power factor (PF) and overall ZT value of the SnTe-based thermoelectric material. The introduction of Bi2O3 forms plenty of SnO2, Bi2O3, and Bi-rich nanoprecipitates. These interfaces between the SnTe matrix and the nanoprecipitates can enhance the average PF through the energy filtering effect. On the other hand, abundant and diverse nanoprecipitates can significantly diminish the lattice thermal conductivity (κlat) through enhanced phonon scattering. The synergistic effect of Bi2O3 resulted in a maximum ZT (ZTmax) value of 0.9 at SnTe-2% Bi2O3 and an average ZT (ZTave) value of 0.4 for SnTe-4% Bi2O3 from 300 K to 823 K. The work provides an excellent reference to develop non-toxic high-performance TE materials.","lang":"eng"}]},{"project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","article_number":"110580","month":"03","has_accepted_license":"1","publication":"Cell Reports","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2211-1247"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","date_published":"2022-03-29T00:00:00Z","file":[{"file_name":"2022_CellReports_Kaneko.pdf","content_type":"application/pdf","date_updated":"2022-04-15T11:00:58Z","file_size":4774216,"checksum":"49105c6c27c9af0f37f50a8bbb4d380d","date_created":"2022-04-15T11:00:58Z","creator":"dernst","file_id":"11172","success":1,"relation":"main_file","access_level":"open_access"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","date_created":"2022-04-10T22:01:39Z","department":[{"_id":"TiVo"}],"publication_status":"published","intvolume":"        38","title":"Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"11143","issue":"13","author":[{"last_name":"Kaneko","first_name":"Keisuke","full_name":"Kaneko, Keisuke"},{"first_name":"Christopher","last_name":"Currin","orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9"},{"full_name":"Goff, Kevin M.","first_name":"Kevin M.","last_name":"Goff"},{"first_name":"Eric R.","last_name":"Wengert","full_name":"Wengert, Eric R."},{"first_name":"Ala","last_name":"Somarowthu","full_name":"Somarowthu, Ala"},{"last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"first_name":"Ethan M.","last_name":"Goldberg","full_name":"Goldberg, Ethan M."}],"publisher":"Elsevier","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-04-15T11:00:58Z","day":"29","doi":"10.1016/j.celrep.2022.110580","abstract":[{"lang":"eng","text":"Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology."}],"year":"2022","citation":{"ieee":"K. Kaneko <i>et al.</i>, “Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome,” <i>Cell Reports</i>, vol. 38, no. 13. Elsevier, 2022.","chicago":"Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>.","apa":"Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels, T. P., &#38; Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>","ama":"Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. 2022;38(13). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>","ista":"Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13), 110580.","mla":"Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>, vol. 38, no. 13, 110580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>.","short":"K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels, E.M. Goldberg, Cell Reports 38 (2022)."},"date_updated":"2023-08-03T06:32:55Z","external_id":{"isi":["000779794000001"]},"isi":1,"volume":38,"acknowledgement":"We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry for comments on a previous version of the manuscript; Xiaohong Zhang for expert technical support and mouse colony maintenance; Melody Cheng for assistance with generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/− mice. This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.), an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was prepared using BioRender software (BioRender.com).","ddc":["570"]},{"scopus_import":"1","_id":"11144","pmid":1,"issue":"6587","author":[{"last_name":"Su","first_name":"Lizhong","full_name":"Su, Lizhong"},{"first_name":"Dongyang","last_name":"Wang","full_name":"Wang, Dongyang"},{"full_name":"Wang, Sining","first_name":"Sining","last_name":"Wang"},{"full_name":"Qin, Bingchao","first_name":"Bingchao","last_name":"Qin"},{"last_name":"Wang","first_name":"Yuping","full_name":"Wang, Yuping"},{"full_name":"Qin, Yongxin","first_name":"Yongxin","last_name":"Qin"},{"full_name":"Jin, Yang","first_name":"Yang","last_name":"Jin"},{"orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"}],"date_created":"2022-04-10T22:01:40Z","article_processing_charge":"No","department":[{"_id":"MaIb"}],"publication_status":"published","intvolume":"       375","title":"High thermoelectric performance realized through manipulating layered phonon-electron decoupling","quality_controlled":"1","page":"1385-1389","publisher":"American Association for the Advancement of Science","article_type":"original","year":"2022","citation":{"ama":"Su L, Wang D, Wang S, et al. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. <i>Science</i>. 2022;375(6587):1385-1389. doi:<a href=\"https://doi.org/10.1126/science.abn8997\">10.1126/science.abn8997</a>","apa":"Su, L., Wang, D., Wang, S., Qin, B., Wang, Y., Qin, Y., … Zhao, L. D. (2022). High thermoelectric performance realized through manipulating layered phonon-electron decoupling. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abn8997\">https://doi.org/10.1126/science.abn8997</a>","ieee":"L. Su <i>et al.</i>, “High thermoelectric performance realized through manipulating layered phonon-electron decoupling,” <i>Science</i>, vol. 375, no. 6587. American Association for the Advancement of Science, pp. 1385–1389, 2022.","chicago":"Su, Lizhong, Dongyang Wang, Sining Wang, Bingchao Qin, Yuping Wang, Yongxin Qin, Yang Jin, Cheng Chang, and Li Dong Zhao. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abn8997\">https://doi.org/10.1126/science.abn8997</a>.","mla":"Su, Lizhong, et al. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” <i>Science</i>, vol. 375, no. 6587, American Association for the Advancement of Science, 2022, pp. 1385–89, doi:<a href=\"https://doi.org/10.1126/science.abn8997\">10.1126/science.abn8997</a>.","short":"L. Su, D. Wang, S. Wang, B. Qin, Y. Wang, Y. Qin, Y. Jin, C. Chang, L.D. Zhao, Science 375 (2022) 1385–1389.","ista":"Su L, Wang D, Wang S, Qin B, Wang Y, Qin Y, Jin Y, Chang C, Zhao LD. 2022. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. Science. 375(6587), 1385–1389."},"date_updated":"2023-10-16T09:10:36Z","external_id":{"pmid":["35324303"],"isi":["000778894800038"]},"isi":1,"day":"25","doi":"10.1126/science.abn8997","abstract":[{"text":"Thermoelectric materials allow for direct conversion between heat and electricity, offering the potential for power generation. The average dimensionless figure of merit ZTave determines device efficiency. N-type tin selenide crystals exhibit outstanding three-dimensional charge and two-dimensional phonon transport along the out-of-plane direction, contributing to a high maximum figure of merit Zmax of ~3.6 × 10−3 per kelvin but a moderate ZTave of ~1.1. We found an attractive high Zmax of ~4.1 × 10−3 per kelvin at 748 kelvin and a ZTave of ~1.7 at 300 to 773 kelvin in chlorine-doped and lead-alloyed tin selenide crystals by phonon-electron decoupling. The chlorine-induced low deformation potential improved the carrier mobility. The lead-induced mass and strain fluctuations reduced the lattice thermal conductivity. Phonon-electron decoupling plays a critical role to achieve high-performance thermoelectrics.","lang":"eng"}],"volume":375,"acknowledgement":"This work was supported by the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Key Research and Development Program of China (2018YFA0702100), the National Science Fund for Distinguished Young Scholars (51925101), the 111 Project (B17002), the Lise Meitner Project (M2889-N), and the National Key Research and Development Program of China (2018YFB0703600). This work is also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.-D.Z. is thankful for the high-performance computing resources at Beihang University.","publication":"Science","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"oa_version":"None","month":"03","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-03-25T00:00:00Z","publication_identifier":{"eissn":["1095-9203"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":"      2022","title":"List-decodability with large radius for Reed-Solomon codes","department":[{"_id":"MaKw"}],"article_processing_charge":"No","date_created":"2022-04-10T22:01:40Z","publication_status":"published","author":[{"last_name":"Ferber","first_name":"Asaf","full_name":"Ferber, Asaf"},{"orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"full_name":"Sauermann, Lisa","first_name":"Lisa","last_name":"Sauermann"}],"scopus_import":"1","_id":"11145","publisher":"IEEE","quality_controlled":"1","page":"720-726","abstract":[{"lang":"eng","text":"List-decodability of Reed-Solomon codes has re-ceived a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r=1−ε for ε tending to zero. Our main result states that there exist Reed-Solomon codes with rate Ω(ε) which are (1−ε,O(1/ε) -list-decodable, meaning that any Hamming ball of radius 1−ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance."}],"day":"01","doi":"10.1109/FOCS52979.2021.00075","arxiv":1,"external_id":{"isi":["000802209600065"],"arxiv":["2012.10584"]},"isi":1,"citation":{"chicago":"Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability with Large Radius for Reed-Solomon Codes.” In <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, 2022:720–26. IEEE, 2022. <a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">https://doi.org/10.1109/FOCS52979.2021.00075</a>.","ieee":"A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius for Reed-Solomon codes,” in <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, Denver, CO, United States, 2022, vol. 2022, pp. 720–726.","apa":"Ferber, A., Kwan, M. A., &#38; Sauermann, L. (2022). List-decodability with large radius for Reed-Solomon codes. In <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i> (Vol. 2022, pp. 720–726). Denver, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">https://doi.org/10.1109/FOCS52979.2021.00075</a>","ama":"Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon codes. In: <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>. Vol 2022. IEEE; 2022:720-726. doi:<a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">10.1109/FOCS52979.2021.00075</a>","ista":"Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius for Reed-Solomon codes. 62nd Annual IEEE Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science vol. 2022, 720–726.","short":"A. Ferber, M.A. Kwan, L. Sauermann, in:, 62nd Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2022, pp. 720–726.","mla":"Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, vol. 2022, IEEE, 2022, pp. 720–26, doi:<a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">10.1109/FOCS52979.2021.00075</a>."},"year":"2022","date_updated":"2023-08-03T06:57:02Z","volume":2022,"month":"02","oa_version":"Preprint","publication":"62nd Annual IEEE Symposium on Foundations of Computer Science","conference":{"location":"Denver, CO, United States","end_date":"2022-02-10","start_date":"2022-02-07","name":"FOCS: Symposium on Foundations of Computer Science"},"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["0272-5428"],"isbn":["9781665420556"]},"type":"conference","date_published":"2022-02-01T00:00:00Z","status":"public","related_material":{"record":[{"status":"public","relation":"later_version","id":"10775"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2012.10584","open_access":"1"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"content_type":"application/pdf","file_name":"2022_JourStructuralBiology_Obr.pdf","date_updated":"2022-08-02T11:07:58Z","file_size":7080863,"checksum":"0b1eb53447aae8e95ae4c12d193b0b00","date_created":"2022-08-02T11:07:58Z","creator":"dernst","file_id":"11722","access_level":"open_access","success":1,"relation":"main_file"}],"oa":1,"publication_identifier":{"issn":["1047-8477"]},"date_published":"2022-06-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"keyword":["Structural Biology"],"month":"06","article_number":"107852","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"publication":"Journal of Structural Biology","has_accepted_license":"1","ddc":["570"],"volume":214,"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"doi":"10.1016/j.jsb.2022.107852","day":"01","isi":1,"external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"date_updated":"2023-08-03T06:25:23Z","citation":{"ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>.","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>.","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>"},"year":"2022","article_type":"original","publisher":"Elsevier","file_date_updated":"2022-08-02T11:07:58Z","quality_controlled":"1","title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","intvolume":"       214","publication_status":"published","date_created":"2022-04-15T07:10:26Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"FlSc"}],"author":[{"full_name":"Obr, Martin","last_name":"Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hagen, Wim J.H.","last_name":"Hagen","first_name":"Wim J.H."},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"full_name":"Yu, Lingbo","first_name":"Lingbo","last_name":"Yu"},{"last_name":"Kotecha","first_name":"Abhay","full_name":"Kotecha, Abhay"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"issue":"2","pmid":1,"_id":"11155","scopus_import":"1"},{"has_accepted_license":"1","publication":"Cell Reports","project":[{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205","call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_number":"110615","month":"04","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-04-05T00:00:00Z","publication_identifier":{"issn":["2211-1247"]},"oa":1,"file":[{"content_type":"application/pdf","file_name":"2022_CellReports_Villa.pdf","date_updated":"2022-04-15T09:06:25Z","file_size":"7808644","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","date_created":"2022-04-15T09:06:25Z","creator":"dernst","file_id":"11164","success":1,"access_level":"open_access","relation":"main_file"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12364"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","pmid":1,"_id":"11160","issue":"1","author":[{"first_name":"Carlo Emanuele","last_name":"Villa","full_name":"Villa, Carlo Emanuele"},{"full_name":"Cheroni, Cristina","last_name":"Cheroni","first_name":"Cristina"},{"first_name":"Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"López-Tóbon","first_name":"Alejandro","full_name":"López-Tóbon, Alejandro"},{"first_name":"Bárbara","last_name":"Oliveira","full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aysan Çerağ","last_name":"Yahya","full_name":"Yahya, Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin"},{"first_name":"Michele","last_name":"Gabriele","full_name":"Gabriele, Michele"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"first_name":"Mariano","last_name":"Gabitto","full_name":"Gabitto, Mariano"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Testa, Giuseppe","first_name":"Giuseppe","last_name":"Testa"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"department":[{"_id":"JoDa"},{"_id":"GaNo"}],"date_created":"2022-04-15T09:03:10Z","article_processing_charge":"Yes","publication_status":"published","intvolume":"        39","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-04-15T09:06:25Z","publisher":"Elsevier","article_type":"original","citation":{"mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022."},"year":"2022","date_updated":"2024-03-25T23:30:25Z","external_id":{"isi":["000785983900003"],"pmid":["35385734"]},"isi":1,"day":"05","doi":"10.1016/j.celrep.2022.110615","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"volume":39,"acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","ddc":["570"]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"creator":"dernst","file_id":"11725","success":1,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","date_updated":"2022-08-05T05:56:03Z","file_size":815607,"checksum":"72bdde48853643a32d42b75f54965c44","date_created":"2022-08-05T05:56:03Z"}],"type":"journal_article","date_published":"2022-06-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["0959-440X"]},"keyword":["Molecular Biology","Structural Biology"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Current Opinion in Structural Biology","article_number":"102350","month":"06","oa_version":"Published Version","ddc":["570"],"volume":74,"external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"isi":1,"citation":{"ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>","ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>.","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350."},"year":"2022","date_updated":"2023-08-03T06:31:06Z","abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"day":"01","doi":"10.1016/j.sbi.2022.102350","file_date_updated":"2022-08-05T05:56:03Z","quality_controlled":"1","article_type":"original","publisher":"Elsevier","author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen","last_name":"Kampjut","first_name":"Domen"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","pmid":1,"_id":"11167","intvolume":"        74","title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","department":[{"_id":"LeSa"}],"date_created":"2022-04-15T09:32:35Z","article_processing_charge":"Yes (via OA deal)","publication_status":"published"},{"date_published":"2022-04-08T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31243-1","relation":"erratum"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"11348","creator":"dernst","relation":"main_file","success":1,"access_level":"open_access","date_updated":"2022-05-02T08:48:00Z","file_name":"2022_NatureCommunications_Gauto.pdf","content_type":"application/pdf","date_created":"2022-05-02T08:48:00Z","file_size":2637590,"checksum":"db61d5534e988743d6266d3675d77b08"}],"publication":"Nature Communications","has_accepted_license":"1","month":"04","article_number":"1927","oa_version":"Published Version","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000781498700009"]},"date_updated":"2023-08-03T06:54:56Z","citation":{"ista":"Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.","short":"D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel, J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).","mla":"Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>, vol. 13, 1927, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni, Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>.","ama":"Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>","apa":"Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I., … Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>"},"year":"2022","abstract":[{"lang":"eng","text":"Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution."}],"doi":"10.1038/s41467-022-29423-0","day":"08","ddc":["570"],"acknowledgement":"We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien Favier for excellent NMR\r\nplatform operation and management. The plasmid coding for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble). We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.).","volume":13,"author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"full_name":"Malinverni, Duccio","first_name":"Duccio","last_name":"Malinverni"},{"first_name":"Hugo","last_name":"Fraga","full_name":"Fraga, Hugo"},{"first_name":"Matteo","last_name":"Paloni","full_name":"Paloni, Matteo"},{"full_name":"Sučec, Iva","last_name":"Sučec","first_name":"Iva"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"first_name":"Juan Pablo","last_name":"Bustamante","full_name":"Bustamante, Juan Pablo"},{"last_name":"Barducci","first_name":"Alessandro","full_name":"Barducci, Alessandro"},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"_id":"11179","scopus_import":"1","title":"Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR","intvolume":"        13","publication_status":"published","article_processing_charge":"No","department":[{"_id":"PaSc"}],"date_created":"2022-04-17T22:01:45Z","file_date_updated":"2022-05-02T08:48:00Z","quality_controlled":"1","article_type":"original","publisher":"Springer Nature"},{"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.00657"}],"related_material":{"record":[{"status":"public","id":"13076","relation":"research_data"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"isbn":["9781450392044"]},"oa":1,"date_published":"2022-04-02T00:00:00Z","type":"conference","conference":{"location":"Seoul, Republic of Korea","end_date":"2022-04-06","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2022-04-02"},"language":[{"iso":"eng"}],"oa_version":"Preprint","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"month":"04","publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","acknowledgement":"We would like to thank the anonymous reviewers for their useful comments. 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 805223 ScaleML).","doi":"10.1145/3503221.3508432","arxiv":1,"day":"02","abstract":[{"text":"Designing and implementing efficient parallel priority schedulers is an active research area. An intriguing proposed design is the Multi-Queue: given n threads and m ≥ n distinct priority queues, task insertions are performed uniformly at random, while, to delete, a thread picks two queues uniformly at random, and removes the observed task of higher priority. This approach scales well, and has probabilistic rank guarantees: roughly, the rank of each task removed, relative to remaining tasks in all other queues, is O (m) in expectation. Yet, the performance of this pattern is below that of well-engineered schedulers, which eschew theoretical guarantees for practical efficiency.\r\n\r\nWe investigate whether it is possible to design and implement a Multi-Queue-based task scheduler that is both highly-efficient and has analytical guarantees. We propose a new variant called the Stealing Multi-Queue (SMQ), a cache-efficient variant of the Multi-Queue, which leverages both queue affinity---each thread has a local queue, from which tasks are usually removed; but, with some probability, threads also attempt to steal higher-priority tasks from the other queues---and task batching, that is, the processing of several tasks in a single insert / remove step. These ideas are well-known for task scheduling without priorities; our theoretical contribution is showing that, despite relaxations, this design can still provide rank guarantees, which in turn implies bounds on total work performed. We provide a general SMQ implementation which can surpass state-of-the-art schedulers such as OBIM and PMOD in terms of performance on popular graph-processing benchmarks. Notably, the performance improvement comes mainly from the superior rank guarantees provided by our scheduler, confirming that analytically-reasoned approaches can still provide performance improvements for priority task scheduling.","lang":"eng"}],"date_updated":"2023-08-03T06:48:35Z","year":"2022","citation":{"ista":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 353–367.","mla":"Postnikova, Anastasiia, et al. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2022, pp. 353–67, doi:<a href=\"https://doi.org/10.1145/3503221.3508432\">10.1145/3503221.3508432</a>.","short":"A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 353–367.","ieee":"A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers,” in <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Seoul, Republic of Korea, 2022, pp. 353–367.","chicago":"Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 353–67. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3503221.3508432\">https://doi.org/10.1145/3503221.3508432</a>.","ama":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. In: <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2022:353-367. doi:<a href=\"https://doi.org/10.1145/3503221.3508432\">10.1145/3503221.3508432</a>","apa":"Postnikova, A., Koval, N., Nadiradze, G., &#38; Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 353–367). Seoul, Republic of Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3503221.3508432\">https://doi.org/10.1145/3503221.3508432</a>"},"isi":1,"external_id":{"isi":["000883318200025"],"arxiv":["2109.00657"]},"publisher":"Association for Computing Machinery","page":"353-367","quality_controlled":"1","ec_funded":1,"publication_status":"published","date_created":"2022-04-17T22:01:46Z","article_processing_charge":"No","department":[{"_id":"DaAl"}],"title":"Multi-queues can be state-of-the-art priority schedulers","_id":"11180","scopus_import":"1","author":[{"full_name":"Postnikova, Anastasiia","first_name":"Anastasiia","last_name":"Postnikova"},{"last_name":"Koval","first_name":"Nikita","full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}]},{"file":[{"date_updated":"2022-08-05T09:19:29Z","file_name":"2022_PPoPP_Brown.pdf","content_type":"application/pdf","date_created":"2022-08-05T09:19:29Z","file_size":1128343,"checksum":"8ceea411fa133795cd4903529498eb6b","file_id":"11731","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"isbn":["9781450392044"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","date_published":"2022-04-02T00:00:00Z","conference":{"location":"Seoul, Republic of Korea","end_date":"2022-04-06","start_date":"2022-04-02","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"04","has_accepted_license":"1","publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development grant: CRDPJ 539431-19, the\r\nCanada Foundation for Innovation John R. Evans Leaders Fund with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512, Waterloo Huawei Joint Innovation Lab project “Scalable Infrastructure for Next Generation Data Management Systems”, NSERC Discovery Launch Supplement: DGECR-2019-00048, NSERC Discovery\r\nProgram under the grants: RGPIN-2019-04227 and RGPIN04512-2018, and the University of Waterloo. We would also like to thank the reviewers for their insightful comments.","ddc":["000"],"day":"02","doi":"10.1145/3503221.3508410","abstract":[{"text":"To maximize the performance of concurrent data structures, researchers have often turned to highly complex fine-grained techniques, resulting in efficient and elegant algorithms, which can however be often difficult to understand and prove correct. While simpler techniques exist, such as transactional memory, they can have limited performance or portability relative to their fine-grained counterparts. Approaches at both ends of this complexity-performance spectrum have been extensively explored, but relatively less is known about the middle ground: approaches that are willing to sacrifice some performance for simplicity, while remaining competitive with state-of-the-art handcrafted designs. In this paper, we explore this middle ground, and present PathCAS, a primitive that combines ideas from multi-word CAS (KCAS) and transactional memory approaches, while carefully avoiding overhead. We show how PathCAS can be used to implement efficient search data structures relatively simply, using an internal binary search tree as an example, then extending this to an AVL tree. Our best implementations outperform many handcrafted search trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known concurrent binary tree in terms of search performance [3]. Our results suggest that PathCAS can yield concurrent data structures that are relatively easy to build and prove correct, while offering surprisingly high performance.","lang":"eng"}],"citation":{"short":"T.A. Brown, W. Sigouin, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 385–399.","mla":"Brown, Trevor A., et al. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2022, pp. 385–99, doi:<a href=\"https://doi.org/10.1145/3503221.3508410\">10.1145/3503221.3508410</a>.","ista":"Brown TA, Sigouin W, Alistarh D-A. 2022. PathCAS: An efficient middle ground for concurrent search data structures. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 385–399.","apa":"Brown, T. A., Sigouin, W., &#38; Alistarh, D.-A. (2022). PathCAS: An efficient middle ground for concurrent search data structures. In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 385–399). Seoul, Republic of Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3503221.3508410\">https://doi.org/10.1145/3503221.3508410</a>","ama":"Brown TA, Sigouin W, Alistarh D-A. PathCAS: An efficient middle ground for concurrent search data structures. In: <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2022:385-399. doi:<a href=\"https://doi.org/10.1145/3503221.3508410\">10.1145/3503221.3508410</a>","chicago":"Brown, Trevor A, William Sigouin, and Dan-Adrian Alistarh. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 385–99. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3503221.3508410\">https://doi.org/10.1145/3503221.3508410</a>.","ieee":"T. A. Brown, W. Sigouin, and D.-A. Alistarh, “PathCAS: An efficient middle ground for concurrent search data structures,” in <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Seoul, Republic of Korea, 2022, pp. 385–399."},"year":"2022","date_updated":"2023-08-03T06:49:20Z","external_id":{"isi":["000883318200027"]},"isi":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","page":"385-399","file_date_updated":"2022-08-05T09:19:29Z","date_created":"2022-04-17T22:01:46Z","article_processing_charge":"No","department":[{"_id":"DaAl"}],"publication_status":"published","title":"PathCAS: An efficient middle ground for concurrent search data structures","scopus_import":"1","_id":"11181","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Sigouin, William","first_name":"William","last_name":"Sigouin"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"date_updated":"2022-05-02T08:16:10Z","file_name":"2022_CurrentProtocols_Kroll.pdf","content_type":"application/pdf","date_created":"2022-05-02T08:16:10Z","checksum":"72152d005c367777f6cf2f6a477f0d52","file_size":2142703,"file_id":"11347","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access"}],"date_published":"2022-04-05T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2691-1299"]},"language":[{"iso":"eng"}],"publication":"Current Protocols","has_accepted_license":"1","month":"04","article_number":"e407","oa_version":"Published Version","ddc":["570"],"acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","volume":2,"external_id":{"pmid":["35384410"]},"date_updated":"2022-05-02T08:18:00Z","year":"2022","citation":{"apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., &#38; Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. Wiley. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. 2022;2(4). doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” <i>Current Protocols</i>, vol. 2, no. 4. Wiley, 2022.","chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>.","mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>, vol. 2, no. 4, e407, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407."},"abstract":[{"text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity.","lang":"eng"}],"doi":"10.1002/cpz1.407","day":"05","file_date_updated":"2022-05-02T08:16:10Z","quality_controlled":"1","article_type":"original","publisher":"Wiley","author":[{"full_name":"Kroll, Janina","first_name":"Janina","last_name":"Kroll"},{"full_name":"Ruiz-Fernandez, Mauricio J.A.","last_name":"Ruiz-Fernandez","first_name":"Mauricio J.A."},{"first_name":"Malte B.","last_name":"Braun","full_name":"Braun, Malte B."},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369"}],"issue":"4","_id":"11182","pmid":1,"scopus_import":"1","title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","intvolume":"         2","publication_status":"published","article_processing_charge":"No","date_created":"2022-04-17T22:01:46Z","department":[{"_id":"NanoFab"}]},{"file":[{"access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"11345","file_size":790396,"checksum":"626551c14de5d4091573200ed0535752","date_created":"2022-05-02T07:53:00Z","file_name":"2022_LIPICs_Nikabadi.pdf","content_type":"application/pdf","date_updated":"2022-05-02T07:53:00Z"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","date_published":"2022-02-01T00:00:00Z","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772198"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2021-12-13","name":"OPODIS","location":"Strasbourg, France","end_date":"2021-12-15"},"has_accepted_license":"1","publication":"25th International Conference on Principles of Distributed Systems","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_number":"15","month":"02","acknowledgement":"Amir Nikabadi: Supported by the LABEX MILYON (ANR-10-LABX-0070) of Université de Lyon, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR). Janne H. Korhonen: Supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).\r\nWe thank François Le Gall and Masayuki Miyamoto for sharing their work on lower bounds for induced subgraph detection [36].","volume":217,"ddc":["510"],"year":"2022","citation":{"ista":"Nikabadi A, Korhonen J. 2022. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 15.","mla":"Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas et al., vol. 217, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">10.4230/LIPIcs.OPODIS.2021.15</a>.","short":"A. Nikabadi, J. Korhonen, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","chicago":"Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” In <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.15</a>.","ieee":"A. Nikabadi and J. Korhonen, “Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters,” in <i>25th International Conference on Principles of Distributed Systems</i>, Strasbourg, France, 2022, vol. 217.","ama":"Nikabadi A, Korhonen J. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In: Bramas Q, Gramoli V, Milani A, eds. <i>25th International Conference on Principles of Distributed Systems</i>. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">10.4230/LIPIcs.OPODIS.2021.15</a>","apa":"Nikabadi, A., &#38; Korhonen, J. (2022). Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In Q. Bramas, V. Gramoli, &#38; A. Milani (Eds.), <i>25th International Conference on Principles of Distributed Systems</i> (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.15</a>"},"date_updated":"2022-05-02T07:56:35Z","day":"01","doi":"10.4230/LIPIcs.OPODIS.2021.15","abstract":[{"lang":"eng","text":"Subgraph detection has recently been one of the most studied problems in the CONGEST model of distributed computing. In this work, we study the distributed complexity of problems closely related to subgraph detection, mainly focusing on induced subgraph detection. The main line of this work presents lower bounds and parameterized algorithms w.r.t structural parameters of the input graph:\r\n- On general graphs, we give unconditional lower bounds for induced detection of cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions from centralized parameterized complexity, we prove lower bounds in CONGEST for detecting patterns with a 4-clique, and for induced path detection conditional on the hardness of triangle detection in the congested clique.\r\n- On graphs of bounded degeneracy, we show that induced paths can be detected fast in CONGEST using techniques from parameterized algorithms, while detecting cycles and patterns of treewidth 2 is hard.\r\n- On graphs of bounded vertex cover number, we show that induced subgraph detection is easy in CONGEST for any pattern graph. More specifically, we adapt a centralized parameterized algorithm for a more general maximum common induced subgraph detection problem to the distributed setting. In addition to these induced subgraph detection results, we study various related problems in the CONGEST and congested clique models, including for multicolored versions of subgraph-detection-like problems."}],"ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-05-02T07:53:00Z","editor":[{"full_name":"Bramas, Quentin","first_name":"Quentin","last_name":"Bramas"},{"full_name":"Gramoli, Vincent","first_name":"Vincent","last_name":"Gramoli"},{"first_name":"Alessia","last_name":"Milani","full_name":"Milani, Alessia"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","_id":"11183","author":[{"last_name":"Nikabadi","first_name":"Amir","full_name":"Nikabadi, Amir"},{"last_name":"Korhonen","first_name":"Janne","full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"}],"department":[{"_id":"DaAl"}],"date_created":"2022-04-17T22:01:47Z","article_processing_charge":"No","publication_status":"published","intvolume":"       217","alternative_title":["LIPIcs"],"title":"Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters"},{"acknowledgement":"Dan Alistarh: This project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant agreement No.805223 ScaleML).\r\nJoel Rybicki: This project has received from the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.\r\nAcknowledgements We grateful to Giorgi Nadiradze for pointing out a generalisation of the phase clock construction to non-regular graphs. We also thank anonymous reviewers for their useful comments on earlier versions of this manuscript.","volume":217,"ddc":["510"],"date_updated":"2022-05-02T08:09:39Z","year":"2022","citation":{"short":"D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","mla":"Alistarh, Dan-Adrian, et al. “Fast Graphical Population Protocols.” <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas et al., vol. 217, 14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">10.4230/LIPIcs.OPODIS.2021.14</a>.","ista":"Alistarh D-A, Gelashvili R, Rybicki J. 2022. Fast graphical population protocols. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 14.","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Rybicki, J. (2022). Fast graphical population protocols. In Q. Bramas, V. Gramoli, &#38; A. Milani (Eds.), <i>25th International Conference on Principles of Distributed Systems</i> (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.14</a>","ama":"Alistarh D-A, Gelashvili R, Rybicki J. Fast graphical population protocols. In: Bramas Q, Gramoli V, Milani A, eds. <i>25th International Conference on Principles of Distributed Systems</i>. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">10.4230/LIPIcs.OPODIS.2021.14</a>","ieee":"D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Fast graphical population protocols,” in <i>25th International Conference on Principles of Distributed Systems</i>, Strasbourg, France, 2022, vol. 217.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Fast Graphical Population Protocols.” In <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.14</a>."},"external_id":{"arxiv":["2102.08808"]},"doi":"10.4230/LIPIcs.OPODIS.2021.14","arxiv":1,"day":"01","abstract":[{"text":"Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node.\r\nIn this work, we consider the more general setting where G is an arbitrary regular graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As a sample application, we show that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties. We believe our results will prove generally useful, as they allow efficient technology transfer between the well-mixed (clique) case, and the under-explored spatial setting.","lang":"eng"}],"ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-05-02T08:06:33Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","editor":[{"first_name":"Quentin","last_name":"Bramas","full_name":"Bramas, Quentin"},{"full_name":"Gramoli, Vincent","last_name":"Gramoli","first_name":"Vincent"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"}],"_id":"11184","scopus_import":"1","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"first_name":"Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"DaAl"}],"date_created":"2022-04-17T22:01:47Z","alternative_title":["LIPIcs"],"title":"Fast graphical population protocols","intvolume":"       217","file":[{"file_name":"2022_LIPICs_Alistarh.pdf","content_type":"application/pdf","date_updated":"2022-05-02T08:06:33Z","checksum":"2c7c982174c6f98c4ca6e92539d15086","file_size":959406,"date_created":"2022-05-02T08:06:33Z","creator":"dernst","file_id":"11346","success":1,"relation":"main_file","access_level":"open_access"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-02-01T00:00:00Z","type":"conference","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772198"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Strasbourg, France","end_date":"2021-12-15","name":"OPODIS","start_date":"2021-12-13"},"publication":"25th International Conference on Principles of Distributed Systems","has_accepted_license":"1","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"},{"grant_number":"840605","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"month":"02","article_number":"14"},{"conference":{"location":"Jember, Indonesia","end_date":"2022-03-26","start_date":"2022-03-24","name":"WALCOM: Algorithms and Computation"},"language":[{"iso":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"oa_version":"Preprint","month":"03","publication":"WALCOM 2022: Algorithms and Computation","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.14892","open_access":"1"}],"status":"public","related_material":{"record":[{"status":"public","id":"13969","relation":"later_version"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030967307"]},"oa":1,"type":"conference","date_published":"2022-03-16T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","ec_funded":1,"series_title":"LNCS","page":"383-395","department":[{"_id":"UlWa"}],"article_processing_charge":"No","date_created":"2022-04-17T22:01:47Z","publication_status":"published","intvolume":"     13174","title":"Approximating the bundled crossing number","scopus_import":"1","_id":"11185","author":[{"last_name":"Arroyo Guevara","first_name":"Alan M","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Felsner","first_name":"Stefan","full_name":"Felsner, Stefan"}],"acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1.","volume":13174,"day":"16","doi":"10.1007/978-3-030-96731-4_31","arxiv":1,"abstract":[{"lang":"eng","text":"Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider bundlings for families of pseudosegments, i.e., simple curves such that any two have share at most one point at which they cross. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of such instances (up to adding a term depending on the facial structure). This 8-approximation also holds for bundlings of good drawings of graphs. In the special case of circular drawings the approximation factor is 8 (no extra term), this improves upon the 10-approximation of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection graph of the pseudosegments is bipartite."}],"citation":{"ista":"Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number. WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS vol. 13174, 383–395.","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” <i>WALCOM 2022: Algorithms and Computation</i>, vol. 13174, Springer Nature, 2022, pp. 383–95, doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>.","short":"A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation, Springer Nature, 2022, pp. 383–395.","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” In <i>WALCOM 2022: Algorithms and Computation</i>, 13174:383–95. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>.","ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” in <i>WALCOM 2022: Algorithms and Computation</i>, Jember, Indonesia, 2022, vol. 13174, pp. 383–395.","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In: <i>WALCOM 2022: Algorithms and Computation</i>. Vol 13174. LNCS. Springer Nature; 2022:383-395. doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>","apa":"Arroyo Guevara, A. M., &#38; Felsner, S. (2022). Approximating the bundled crossing number. In <i>WALCOM 2022: Algorithms and Computation</i> (Vol. 13174, pp. 383–395). Jember, Indonesia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>"},"year":"2022","date_updated":"2023-09-25T10:56:10Z","external_id":{"arxiv":["2109.14892"]}},{"publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_published":"2022-08-01T00:00:00Z","type":"journal_article","file":[{"date_updated":"2023-02-03T09:43:38Z","content_type":"application/pdf","file_name":"2022_BulletinMathSociety_Kwan.pdf","date_created":"2023-02-03T09:43:38Z","checksum":"02d74e7ae955ba3c808e2a8aebe6ef98","file_size":233758,"file_id":"12499","creator":"dernst","relation":"main_file","access_level":"open_access","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","oa_version":"Published Version","month":"08","publication":"Bulletin of the London Mathematical Society","has_accepted_license":"1","language":[{"iso":"eng"}],"arxiv":1,"doi":"10.1112/blms.12638","day":"01","abstract":[{"lang":"eng","text":"In this note, we study large deviations of the number  𝐍  of intercalates ( 2×2  combinatorial subsquares which are themselves Latin squares) in a random  𝑛×𝑛  Latin square. In particular, for constant  𝛿>0  we prove that  exp(−𝑂(𝑛2log𝑛))⩽Pr(𝐍⩽(1−𝛿)𝑛2/4)⩽exp(−Ω(𝑛2))  and  exp(−𝑂(𝑛4/3(log𝑛)))⩽Pr(𝐍⩾(1+𝛿)𝑛2/4)⩽exp(−Ω(𝑛4/3(log𝑛)2/3)) . As a consequence, we deduce that a typical order- 𝑛  Latin square has  (1+𝑜(1))𝑛2/4  intercalates, matching a lower bound due to Kwan and Sudakov and resolving an old conjecture of McKay and Wanless."}],"date_updated":"2023-08-03T06:47:29Z","citation":{"short":"M.A. Kwan, A. Sah, M. Sawhney, Bulletin of the London Mathematical Society 54 (2022) 1420–1438.","mla":"Kwan, Matthew Alan, et al. “Large Deviations in Random Latin Squares.” <i>Bulletin of the London Mathematical Society</i>, vol. 54, no. 4, Wiley, 2022, pp. 1420–38, doi:<a href=\"https://doi.org/10.1112/blms.12638\">10.1112/blms.12638</a>.","ista":"Kwan MA, Sah A, Sawhney M. 2022. Large deviations in random latin squares. Bulletin of the London Mathematical Society. 54(4), 1420–1438.","ama":"Kwan MA, Sah A, Sawhney M. Large deviations in random latin squares. <i>Bulletin of the London Mathematical Society</i>. 2022;54(4):1420-1438. doi:<a href=\"https://doi.org/10.1112/blms.12638\">10.1112/blms.12638</a>","apa":"Kwan, M. A., Sah, A., &#38; Sawhney, M. (2022). Large deviations in random latin squares. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12638\">https://doi.org/10.1112/blms.12638</a>","ieee":"M. A. Kwan, A. Sah, and M. Sawhney, “Large deviations in random latin squares,” <i>Bulletin of the London Mathematical Society</i>, vol. 54, no. 4. Wiley, pp. 1420–1438, 2022.","chicago":"Kwan, Matthew Alan, Ashwin Sah, and Mehtaab Sawhney. “Large Deviations in Random Latin Squares.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2022. <a href=\"https://doi.org/10.1112/blms.12638\">https://doi.org/10.1112/blms.12638</a>."},"year":"2022","isi":1,"external_id":{"isi":["000779920900001"],"arxiv":["2106.11932"]},"acknowledgement":"We thank Zach Hunter for pointing out some important typographical errors. We also thank the referee for several remarks which helped improve the paper substantially.\r\nKwan was supported by NSF grant DMS-1953990. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302.","volume":54,"ddc":["510"],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"MaKw"}],"date_created":"2022-04-17T22:01:48Z","title":"Large deviations in random latin squares","intvolume":"        54","_id":"11186","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"full_name":"Sah, Ashwin","first_name":"Ashwin","last_name":"Sah"},{"first_name":"Mehtaab","last_name":"Sawhney","full_name":"Sawhney, Mehtaab"}],"issue":"4","publisher":"Wiley","article_type":"original","page":"1420-1438","quality_controlled":"1","file_date_updated":"2023-02-03T09:43:38Z"},{"project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"oa_version":"Published Version","month":"04","publication":"Nature Methods","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"oa":1,"type":"journal_article","date_published":"2022-04-08T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-022-01444-z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-04-17T22:01:48Z","department":[{"_id":"FyKo"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        19","title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","scopus_import":"1","pmid":1,"_id":"11187","issue":"4","author":[{"full_name":"Knyazev, Sergey","last_name":"Knyazev","first_name":"Sergey"},{"first_name":"Karishma","last_name":"Chhugani","full_name":"Chhugani, Karishma"},{"full_name":"Sarwal, Varuni","first_name":"Varuni","last_name":"Sarwal"},{"first_name":"Ram","last_name":"Ayyala","full_name":"Ayyala, Ram"},{"full_name":"Singh, Harman","last_name":"Singh","first_name":"Harman"},{"full_name":"Karthikeyan, Smruthi","first_name":"Smruthi","last_name":"Karthikeyan"},{"full_name":"Deshpande, Dhrithi","last_name":"Deshpande","first_name":"Dhrithi"},{"last_name":"Baykal","first_name":"Pelin Icer","full_name":"Baykal, Pelin Icer"},{"full_name":"Comarova, Zoia","first_name":"Zoia","last_name":"Comarova"},{"first_name":"Angela","last_name":"Lu","full_name":"Lu, Angela"},{"full_name":"Porozov, Yuri","last_name":"Porozov","first_name":"Yuri"},{"full_name":"Vasylyeva, Tetyana I.","last_name":"Vasylyeva","first_name":"Tetyana I."},{"full_name":"Wertheim, Joel O.","first_name":"Joel O.","last_name":"Wertheim"},{"full_name":"Tierney, Braden T.","last_name":"Tierney","first_name":"Braden T."},{"full_name":"Chiu, Charles Y.","last_name":"Chiu","first_name":"Charles Y."},{"first_name":"Ren","last_name":"Sun","full_name":"Sun, Ren"},{"full_name":"Wu, Aiping","last_name":"Wu","first_name":"Aiping"},{"last_name":"Abedalthagafi","first_name":"Malak S.","full_name":"Abedalthagafi, Malak S."},{"last_name":"Pak","first_name":"Victoria M.","full_name":"Pak, Victoria M."},{"full_name":"Nagaraj, Shivashankar H.","first_name":"Shivashankar H.","last_name":"Nagaraj"},{"first_name":"Adam L.","last_name":"Smith","full_name":"Smith, Adam L."},{"full_name":"Skums, Pavel","first_name":"Pavel","last_name":"Skums"},{"full_name":"Pasaniuc, Bogdan","first_name":"Bogdan","last_name":"Pasaniuc"},{"first_name":"Andrey","last_name":"Komissarov","full_name":"Komissarov, Andrey"},{"full_name":"Mason, Christopher E.","last_name":"Mason","first_name":"Christopher E."},{"full_name":"Bortz, Eric","last_name":"Bortz","first_name":"Eric"},{"first_name":"Philippe","last_name":"Lemey","full_name":"Lemey, Philippe"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Niko","last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko"},{"full_name":"Lam, Tommy Tsan Yuk","last_name":"Lam","first_name":"Tommy Tsan Yuk"},{"full_name":"Wu, Nicholas C.","last_name":"Wu","first_name":"Nicholas C."},{"first_name":"Alex","last_name":"Zelikovsky","full_name":"Zelikovsky, Alex"},{"first_name":"Rob","last_name":"Knight","full_name":"Knight, Rob"},{"last_name":"Crandall","first_name":"Keith A.","full_name":"Crandall, Keith A."},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"}],"publisher":"Springer Nature","article_type":"letter_note","quality_controlled":"1","ec_funded":1,"page":"374-380","day":"08","doi":"10.1038/s41592-022-01444-z","abstract":[{"text":"During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.","lang":"eng"}],"year":"2022","citation":{"ista":"Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.","mla":"Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>.","short":"S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.","chicago":"Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>.","ieee":"S. Knyazev <i>et al.</i>, “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” <i>Nature Methods</i>, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022.","ama":"Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. 2022;19(4):374-380. doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>","apa":"Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>"},"date_updated":"2023-08-03T06:46:09Z","external_id":{"pmid":["35396471"],"isi":["000781199600011"]},"isi":1,"volume":19,"acknowledgement":"Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL)."},{"ddc":["570"],"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"day":"20","doi":"10.15479/at:ista:11193","degree_awarded":"PhD","citation":{"ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>.","apa":"Wachner, S. (2022). <i>Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","mla":"Wachner, Stephanie. <i>Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>."},"year":"2022","date_updated":"2023-09-19T10:15:54Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-04-21T22:30:03Z","page":"170","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","date_created":"2022-04-20T08:59:07Z","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"publication_status":"published","author":[{"last_name":"Wachner","first_name":"Stephanie","full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"}],"_id":"11193","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"10614","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"544","status":"public"}]},"file":[{"file_id":"11195","creator":"cchlebak","access_level":"open_access","relation":"main_file","date_updated":"2023-04-21T22:30:03Z","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","content_type":"application/pdf","embargo":"2023-04-20","date_created":"2022-04-20T09:03:57Z","checksum":"999ab16884c4522486136ebc5ae8dbff","file_size":8820951},{"file_size":65864612,"checksum":"fd92b1e38d53bdf8b458213882d41383","embargo_to":"open_access","date_created":"2022-04-22T12:41:00Z","file_name":"Thesis_Stephanie_Wachner_20200414.zip","content_type":"application/x-zip-compressed","date_updated":"2023-04-21T22:30:03Z","relation":"source_file","access_level":"closed","creator":"cchlebak","file_id":"11329"}],"oa":1,"supervisor":[{"first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2022-04-20T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"month":"04","project":[{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"has_accepted_license":"1"},{"day":"20","doi":"10.15479/at:ista:11196","degree_awarded":"PhD","abstract":[{"text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n","lang":"eng"}],"citation":{"ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","mla":"Kim, Olena. <i>Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>.","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>.","apa":"Kim, O. (2022). <i>Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>"},"year":"2022","date_updated":"2023-08-18T06:31:52Z","ddc":["570"],"date_created":"2022-04-20T09:47:12Z","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"article_processing_charge":"No","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","_id":"11196","author":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim","full_name":"Kim, Olena"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"page":"132","file_date_updated":"2023-04-20T22:30:03Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","date_published":"2022-04-20T00:00:00Z","file":[{"relation":"main_file","access_level":"open_access","creator":"okim","file_id":"11220","file_size":21273537,"checksum":"1616a8bf6f13a57c892dac873dcd0936","date_created":"2022-04-20T14:21:56Z","embargo":"2023-04-19","file_name":"Olena_KIM_thesis_final.pdf","content_type":"application/pdf","date_updated":"2023-04-20T22:30:03Z"},{"date_created":"2022-04-20T14:22:56Z","embargo_to":"open_access","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","file_size":59248569,"date_updated":"2023-04-20T22:30:03Z","file_name":"KIM_thesis_final.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"11221","creator":"okim"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"11222","relation":"part_of_dissertation","status":"public"},{"id":"7473","relation":"part_of_dissertation","status":"public"}]},"status":"public","project":[{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"month":"04","has_accepted_license":"1","language":[{"iso":"eng"}]}]