[{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"year":"2022","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2023-09-20T20:58:24Z","publication_status":"published","day":"01","keyword":["autosomal recessive","biallelic variants","C","elegans","translation initiation sites","tryptophanyl-tRNA synthetase 1 (WARS1)","WHEP domain","zebrafish"],"author":[{"last_name":"Lin","first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia"},{"full_name":"Vona, Barbara","first_name":"Barbara","last_name":"Vona"},{"first_name":"Hillary M.","full_name":"Porter, Hillary M.","last_name":"Porter"},{"full_name":"Izadi, Mahmoud","first_name":"Mahmoud","last_name":"Izadi"},{"orcid":"0000-0002-2512-7812","last_name":"Huang","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin"},{"last_name":"Lacassie","full_name":"Lacassie, Yves","first_name":"Yves"},{"full_name":"Rosenfeld, Jill A.","first_name":"Jill A.","last_name":"Rosenfeld"},{"last_name":"Khan","first_name":"Saadullah","full_name":"Khan, Saadullah"},{"last_name":"Petree","first_name":"Cassidy","full_name":"Petree, Cassidy"},{"full_name":"Ali, Tayyiba A.","first_name":"Tayyiba A.","last_name":"Ali"},{"full_name":"Muhammad, Nazif","first_name":"Nazif","last_name":"Muhammad"},{"last_name":"Khan","first_name":"Sher A.","full_name":"Khan, Sher A."},{"last_name":"Muhammad","full_name":"Muhammad, Noor","first_name":"Noor"},{"first_name":"Pengfei","full_name":"Liu, Pengfei","last_name":"Liu"},{"last_name":"Haymon","first_name":"Marie-Louise","full_name":"Haymon, Marie-Louise"},{"last_name":"Rueschendorf","first_name":"Franz","full_name":"Rueschendorf, Franz"},{"first_name":"Il-Keun","full_name":"Kong, Il-Keun","last_name":"Kong"},{"last_name":"Schnapp","full_name":"Schnapp, Linda","first_name":"Linda"},{"first_name":"Natasha","full_name":"Shur, Natasha","last_name":"Shur"},{"full_name":"Chorich, Lynn","first_name":"Lynn","last_name":"Chorich"},{"first_name":"Lawrence","full_name":"Layman, Lawrence","last_name":"Layman"},{"first_name":"Thomas","full_name":"Haaf, Thomas","last_name":"Haaf"},{"last_name":"Pourkarimi","full_name":"Pourkarimi, Ehsan","first_name":"Ehsan"},{"first_name":"Hyung-Goo","full_name":"Kim, Hyung-Goo","last_name":"Kim"},{"last_name":"Varshney","first_name":"Gaurav K.","full_name":"Varshney, Gaurav K."}],"page":"1472-1489","month":"10","extern":"1","file":[{"relation":"main_file","creator":"dernst","date_created":"2023-09-25T08:52:54Z","file_id":"14370","content_type":"application/pdf","file_size":12131312,"date_updated":"2023-09-25T08:52:54Z","checksum":"74b01d4e4084b2f64c30ed32b18ee928","success":1,"access_level":"open_access","file_name":"2022_HumanMutation_Lin.pdf"}],"oa":1,"quality_controlled":"1","article_processing_charge":"No","publication":"Human Mutation","date_updated":"2023-09-25T08:54:14Z","doi":"10.1002/humu.24435","publisher":"Wiley","oa_version":"Published Version","article_type":"original","volume":43,"type":"journal_article","date_published":"2022-10-01T00:00:00Z","file_date_updated":"2023-09-25T08:52:54Z","scopus_import":"1","publication_identifier":{"issn":["1059-7794"]},"issue":"10","abstract":[{"lang":"eng","text":"Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for faithful assignment of amino acids to their cognate tRNA. Variants in ARS genes are frequently associated with clinically heterogeneous phenotypes in humans and follow both autosomal dominant or recessive inheritance patterns in many instances. Variants in tryptophanyl-tRNA synthetase 1 (WARS1) cause autosomal dominantly inherited distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. Presently, only one family with biallelic WARS1 variants has been described. We present three affected individuals from two families with biallelic variants (p.Met1? and p.(Asp419Asn)) in WARS1, showing varying severities of developmental delay and intellectual disability. Hearing impairment and microcephaly, as well as abnormalities of the brain, skeletal system, movement/gait, and behavior were variable features. Phenotyping of knocked down wars-1 in a Caenorhabditis elegans model showed depletion is associated with defects in germ cell development. A wars1 knockout vertebrate model recapitulates the human clinical phenotypes, confirms variant pathogenicity, and uncovers evidence implicating the p.Met1? variant as potentially impacting an exon critical for normal hearing. Together, our findings provide consolidating evidence for biallelic disruption of WARS1 as causal for an autosomal recessive neurodevelopmental syndrome and present a vertebrate model that recapitulates key phenotypes observed in patients."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14356","title":"Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function","has_accepted_license":"1","citation":{"chicago":"Lin, Sheng-Jia, Barbara Vona, Hillary M. Porter, Mahmoud Izadi, Kevin Huang, Yves Lacassie, Jill A. Rosenfeld, et al. “Biallelic Variants in WARS1 Cause a Highly Variable Neurodevelopmental Syndrome and Implicate a Critical Exon for Normal Auditory Function.” <i>Human Mutation</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/humu.24435\">https://doi.org/10.1002/humu.24435</a>.","ama":"Lin S-J, Vona B, Porter HM, et al. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. <i>Human Mutation</i>. 2022;43(10):1472-1489. doi:<a href=\"https://doi.org/10.1002/humu.24435\">10.1002/humu.24435</a>","mla":"Lin, Sheng-Jia, et al. “Biallelic Variants in WARS1 Cause a Highly Variable Neurodevelopmental Syndrome and Implicate a Critical Exon for Normal Auditory Function.” <i>Human Mutation</i>, vol. 43, no. 10, Wiley, 2022, pp. 1472–89, doi:<a href=\"https://doi.org/10.1002/humu.24435\">10.1002/humu.24435</a>.","ieee":"S.-J. Lin <i>et al.</i>, “Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function,” <i>Human Mutation</i>, vol. 43, no. 10. Wiley, pp. 1472–1489, 2022.","short":"S.-J. Lin, B. Vona, H.M. Porter, M. Izadi, K. Huang, Y. Lacassie, J.A. Rosenfeld, S. Khan, C. Petree, T.A. Ali, N. Muhammad, S.A. Khan, N. Muhammad, P. Liu, M.-L. Haymon, F. Rueschendorf, I.-K. Kong, L. Schnapp, N. Shur, L. Chorich, L. Layman, T. Haaf, E. Pourkarimi, H.-G. Kim, G.K. Varshney, Human Mutation 43 (2022) 1472–1489.","ista":"Lin S-J, Vona B, Porter HM, Izadi M, Huang K, Lacassie Y, Rosenfeld JA, Khan S, Petree C, Ali TA, Muhammad N, Khan SA, Muhammad N, Liu P, Haymon M-L, Rueschendorf F, Kong I-K, Schnapp L, Shur N, Chorich L, Layman L, Haaf T, Pourkarimi E, Kim H-G, Varshney GK. 2022. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. 43(10), 1472–1489.","apa":"Lin, S.-J., Vona, B., Porter, H. M., Izadi, M., Huang, K., Lacassie, Y., … Varshney, G. K. (2022). Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. <i>Human Mutation</i>. Wiley. <a href=\"https://doi.org/10.1002/humu.24435\">https://doi.org/10.1002/humu.24435</a>"},"intvolume":"        43","status":"public"},{"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"ddc":["570"],"language":[{"iso":"eng"}],"year":"2022","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2023-09-20T20:59:33Z","publication_status":"published","day":"01","author":[{"last_name":"Boegershausen","full_name":"Boegershausen, Nina","first_name":"Nina"},{"last_name":"Krawczyk","first_name":"Hannah E.","full_name":"Krawczyk, Hannah E."},{"full_name":"Jamra, Rami A.","first_name":"Rami A.","last_name":"Jamra"},{"full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia","last_name":"Lin"},{"last_name":"Yigit","first_name":"Goekhan","full_name":"Yigit, Goekhan"},{"first_name":"Irina","full_name":"Huening, Irina","last_name":"Huening"},{"first_name":"Anna M.","full_name":"Polo, Anna M.","last_name":"Polo"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","first_name":"Kevin","full_name":"Huang, Kevin","last_name":"Huang","orcid":"0000-0002-2512-7812"},{"first_name":"Julia","full_name":"Schmidt, Julia","last_name":"Schmidt"},{"last_name":"Altmueller","first_name":"Janine","full_name":"Altmueller, Janine"},{"full_name":"Luppe, Johannes","first_name":"Johannes","last_name":"Luppe"},{"first_name":"Konrad","full_name":"Platzer, Konrad","last_name":"Platzer"},{"last_name":"Doergeloh","full_name":"Doergeloh, Beate B.","first_name":"Beate B."},{"last_name":"Busche","first_name":"Andreas","full_name":"Busche, Andreas"},{"full_name":"Biskup, Saskia","first_name":"Saskia","last_name":"Biskup"},{"full_name":"Mendes, I, Marisa","first_name":"Marisa","last_name":"Mendes, I"},{"last_name":"Smith","first_name":"Desiree E. C.","full_name":"Smith, Desiree E. C."},{"last_name":"Salomons","full_name":"Salomons, Gajja S.","first_name":"Gajja S."},{"first_name":"Arne","full_name":"Zibat, Arne","last_name":"Zibat"},{"full_name":"Bueltmann, Eva","first_name":"Eva","last_name":"Bueltmann"},{"first_name":"Peter","full_name":"Nuernberg, Peter","last_name":"Nuernberg"},{"first_name":"Malte","full_name":"Spielmann, Malte","last_name":"Spielmann"},{"last_name":"Lemke","full_name":"Lemke, Johannes R.","first_name":"Johannes R."},{"last_name":"Li","first_name":"Yun","full_name":"Li, Yun"},{"last_name":"Zenker","full_name":"Zenker, Martin","first_name":"Martin"},{"full_name":"Varshney, Gaurav K.","first_name":"Gaurav K.","last_name":"Varshney"},{"full_name":"Hillen, Hauke S.","first_name":"Hauke S.","last_name":"Hillen"},{"last_name":"Kratz","full_name":"Kratz, Christian P.","first_name":"Christian P."},{"first_name":"Bernd","full_name":"Wollnik, Bernd","last_name":"Wollnik"}],"keyword":["aminoacylation","aminoacyl-tRNA synthetase","ARS","CRISPR","Cas9","intellectual disability","microcephaly","SARS1","tRNA","WARS1","zebrafish"],"page":"1454-1471","month":"10","extern":"1","oa":1,"file":[{"checksum":"c31fc91e0445c35b9da83eb911a9b552","file_name":"2022_HumanMutation_Boegershausen.pdf","access_level":"open_access","success":1,"file_size":4863605,"date_updated":"2023-09-25T08:41:23Z","file_id":"14367","date_created":"2023-09-25T08:41:23Z","content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"quality_controlled":"1","article_processing_charge":"No","publication":"Human Mutation","date_updated":"2023-09-25T08:43:06Z","publisher":"Wiley","doi":"10.1002/humu.24430","article_type":"original","oa_version":"Published Version","external_id":{"pmid":["35790048"]},"volume":43,"type":"journal_article","date_published":"2022-10-01T00:00:00Z","file_date_updated":"2023-09-25T08:41:23Z","scopus_import":"1","publication_identifier":{"issn":["1059-7794"]},"issue":"10","pmid":1,"abstract":[{"text":"Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme’s active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14357","title":"WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly","has_accepted_license":"1","citation":{"chicago":"Boegershausen, Nina, Hannah E. Krawczyk, Rami A. Jamra, Sheng-Jia Lin, Goekhan Yigit, Irina Huening, Anna M. Polo, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” <i>Human Mutation</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/humu.24430\">https://doi.org/10.1002/humu.24430</a>.","ama":"Boegershausen N, Krawczyk HE, Jamra RA, et al. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. <i>Human Mutation</i>. 2022;43(10):1454-1471. doi:<a href=\"https://doi.org/10.1002/humu.24430\">10.1002/humu.24430</a>","mla":"Boegershausen, Nina, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” <i>Human Mutation</i>, vol. 43, no. 10, Wiley, 2022, pp. 1454–71, doi:<a href=\"https://doi.org/10.1002/humu.24430\">10.1002/humu.24430</a>.","ieee":"N. Boegershausen <i>et al.</i>, “WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly,” <i>Human Mutation</i>, vol. 43, no. 10. Wiley, pp. 1454–1471, 2022.","short":"N. Boegershausen, H.E. Krawczyk, R.A. Jamra, S.-J. Lin, G. Yigit, I. Huening, A.M. Polo, B. Vona, K. Huang, J. Schmidt, J. Altmueller, J. Luppe, K. Platzer, B.B. Doergeloh, A. Busche, S. Biskup, M. Mendes, I, D.E.C. Smith, G.S. Salomons, A. Zibat, E. Bueltmann, P. Nuernberg, M. Spielmann, J.R. Lemke, Y. Li, M. Zenker, G.K. Varshney, H.S. Hillen, C.P. Kratz, B. Wollnik, Human Mutation 43 (2022) 1454–1471.","ista":"Boegershausen N, Krawczyk HE, Jamra RA, Lin S-J, Yigit G, Huening I, Polo AM, Vona B, Huang K, Schmidt J, Altmueller J, Luppe J, Platzer K, Doergeloh BB, Busche A, Biskup S, Mendes, I M, Smith DEC, Salomons GS, Zibat A, Bueltmann E, Nuernberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. 2022. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 43(10), 1454–1471.","apa":"Boegershausen, N., Krawczyk, H. E., Jamra, R. A., Lin, S.-J., Yigit, G., Huening, I., … Wollnik, B. (2022). WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. <i>Human Mutation</i>. Wiley. <a href=\"https://doi.org/10.1002/humu.24430\">https://doi.org/10.1002/humu.24430</a>"},"intvolume":"        43","status":"public"},{"department":[{"_id":"UlWa"}],"year":"2022","language":[{"iso":"eng"}],"scopus_import":"1","publication_status":"published","day":"01","publication_identifier":{"issn":["0037-9484"],"eissn":["2102-622X"]},"date_created":"2023-10-01T22:01:14Z","page":"281-294","author":[{"full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"quality_controlled":"1","month":"01","_id":"14381","publication":"Bulletin de la Societe Mathematique de France","publisher":"Societe Mathematique de France","date_updated":"2023-10-03T08:04:03Z","title":"High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others)","doi":"10.24033/ast.1188","abstract":[{"lang":"eng","text":"Expander graphs (sparse but highly connected graphs) have, since their inception, been the source of deep links between Mathematics and Computer Science as well as applications to other areas. In recent years, a fascinating theory of high-dimensional expanders has begun to emerge, which is still in a formative stage but has nonetheless already lead to a number of striking results. Unlike for graphs, in higher dimensions there is a rich array of non-equivalent notions of expansion (coboundary expansion, cosystolic expansion, topological expansion, spectral expansion, etc.), with differents strengths and applications. In this talk, we will survey this landscape of high-dimensional expansion, with a focus on two main results. First, we will present Gromov’s Topological Overlap Theorem, which asserts that coboundary expansion (a quantitative version of vanishing mod 2 cohomology) implies topological expansion (roughly, the property that for every map from a simplicial complex to a manifold of the same dimension, the images of a positive fraction of the simplices have a point in common). Second, we will outline a construction of bounded degree 2-dimensional topological expanders, due to Kaufman, Kazhdan, and Lubotzky."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"       438","citation":{"mla":"Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” <i>Bulletin de La Societe Mathematique de France</i>, vol. 438, Societe Mathematique de France, 2022, pp. 281–94, doi:<a href=\"https://doi.org/10.24033/ast.1188\">10.24033/ast.1188</a>.","ama":"Wagner U. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). <i>Bulletin de la Societe Mathematique de France</i>. 2022;438:281-294. doi:<a href=\"https://doi.org/10.24033/ast.1188\">10.24033/ast.1188</a>","chicago":"Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” <i>Bulletin de La Societe Mathematique de France</i>. Societe Mathematique de France, 2022. <a href=\"https://doi.org/10.24033/ast.1188\">https://doi.org/10.24033/ast.1188</a>.","apa":"Wagner, U. (2022). High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). <i>Bulletin de La Societe Mathematique de France</i>. Societe Mathematique de France. <a href=\"https://doi.org/10.24033/ast.1188\">https://doi.org/10.24033/ast.1188</a>","ista":"Wagner U. 2022. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). Bulletin de la Societe Mathematique de France. 438, 281–294.","short":"U. Wagner, Bulletin de La Societe Mathematique de France 438 (2022) 281–294.","ieee":"U. Wagner, “High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others),” <i>Bulletin de la Societe Mathematique de France</i>, vol. 438. Societe Mathematique de France, pp. 281–294, 2022."},"oa_version":"None","article_type":"original","status":"public","volume":438,"date_published":"2022-01-01T00:00:00Z","type":"journal_article"},{"article_processing_charge":"No","publication":"Nature","date_updated":"2023-10-18T06:26:30Z","doi":"10.1038/d41586-022-04447-0","publisher":"Springer Nature","month":"12","quality_controlled":"1","volume":612,"type":"journal_article","date_published":"2022-12-21T00:00:00Z","oa_version":"None","external_id":{"pmid":["36543947"]},"article_type":"letter_note","year":"2022","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"author":[{"full_name":"Utzat, Hendrik","first_name":"Hendrik","last_name":"Utzat"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"keyword":["Multidisciplinary"],"page":"638-639","date_created":"2023-10-17T11:14:43Z","publication_status":"published","day":"21","abstract":[{"text":"Future LEDs could be based on lead halide perovskites. A breakthrough in preparing device-compatible solids composed of nanoscale perovskite crystals overcomes a long-standing hurdle in making blue perovskite LEDs.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14437","title":"Molecular engineering enables bright blue LEDs","pmid":1,"status":"public","citation":{"mla":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>, vol. 612, no. 7941, Springer Nature, 2022, pp. 638–39, doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>.","ama":"Utzat H, Ibáñez M. Molecular engineering enables bright blue LEDs. <i>Nature</i>. 2022;612(7941):638-639. doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>","chicago":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>.","apa":"Utzat, H., &#38; Ibáñez, M. (2022). Molecular engineering enables bright blue LEDs. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>","ista":"Utzat H, Ibáñez M. 2022. Molecular engineering enables bright blue LEDs. Nature. 612(7941), 638–639.","short":"H. Utzat, M. Ibáñez, Nature 612 (2022) 638–639.","ieee":"H. Utzat and M. Ibáñez, “Molecular engineering enables bright blue LEDs,” <i>Nature</i>, vol. 612, no. 7941. Springer Nature, pp. 638–639, 2022."},"intvolume":"       612","issue":"7941","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]}},{"date_published":"2022-06-28T00:00:00Z","type":"research_data_reference","status":"public","oa_version":"Published Version","citation":{"chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>.","mla":"Zemlicka, Martin, et al. <i>Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>.","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022).","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>."},"main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.8408897","open_access":"1"}],"has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses\" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request."}],"date_updated":"2024-09-10T12:23:57Z","title":"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses","doi":"10.5281/ZENODO.8408897","publisher":"Zenodo","_id":"14520","month":"06","oa":1,"author":[{"last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628"},{"full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani"},{"last_name":"Trioni","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea"},{"orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-11-13T08:09:10Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"28","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14517"}]},"year":"2022","ddc":["530"],"tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"department":[{"_id":"JoFi"}]},{"day":"31","publication_status":"submitted","date_created":"2023-11-23T09:30:02Z","arxiv":1,"author":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marveggio, Alice","first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio"}],"department":[{"_id":"JuFi"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14587"}]},"language":[{"iso":"eng"}],"year":"2022","citation":{"ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>.","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>.","ista":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>.","apa":"Fischer, J. L., &#38; Marveggio, A. (n.d.). Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>","short":"J.L. Fischer, A. Marveggio, ArXiv (n.d.).","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow,” <i>arXiv</i>. ."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.17143"}],"external_id":{"arxiv":["2203.17143"]},"oa_version":"Preprint","status":"public","ec_funded":1,"type":"preprint","date_published":"2022-03-31T00:00:00Z","project":[{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"oa":1,"month":"03","doi":"10.48550/ARXIV.2203.17143","date_updated":"2023-11-30T13:25:02Z","title":"Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow","_id":"14597","publication":"arXiv","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Phase-field models such as the Allen-Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen-Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow.\r\nIn the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: As long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen-Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε1/2).\r\nOur approach is based on the gradient flow structure of the Allen-Cahn equation and its limiting motion: Building on the recent concept of \"gradient flow calibrations\" for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen-Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen-Cahn operator or additional convergence hypotheses for the energy at positive times."}]},{"author":[{"orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"arxiv":1,"date_created":"2023-11-24T13:10:09Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","day":"29","publication_status":"submitted","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14539"},{"relation":"later_version","status":"public","id":"14830"}]},"year":"2022","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"type":"preprint","date_published":"2022-11-29T00:00:00Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"status":"public","ec_funded":1,"oa_version":"Preprint","external_id":{"arxiv":["2210.05308"]},"citation":{"ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>","mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>.","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">https://doi.org/10.48550/ARXIV.2210.05308</a>.","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>.","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., &#38; Chatterjee, K. (n.d.). Learning control policies for stochastic systems with reach-avoid guarantees. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">https://doi.org/10.48550/ARXIV.2210.05308</a>","short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, ArXiv (n.d.).","ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” <i>arXiv</i>. ."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.05308"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold $p\\in[0,1]$ over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on $3$ stochastic non-linear reinforcement learning tasks.","lang":"eng"}],"doi":"10.48550/ARXIV.2210.05308","title":"Learning control policies for stochastic systems with reach-avoid guarantees","date_updated":"2025-07-14T09:10:02Z","_id":"14600","publication":"arXiv","month":"11","oa":1},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2205.11991"}],"citation":{"ama":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>","mla":"Zikelic, Dorde, et al. “Learning Stabilizing Policies in Stochastic Control Systems.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>.","chicago":"Zikelic, Dorde, Mathias Lechner, Krishnendu Chatterjee, and Thomas A Henzinger. “Learning Stabilizing Policies in Stochastic Control Systems.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">https://doi.org/10.48550/arXiv.2205.11991</a>.","ista":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>.","apa":"Zikelic, D., Lechner, M., Chatterjee, K., &#38; Henzinger, T. A. (n.d.). Learning stabilizing policies in stochastic control systems. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">https://doi.org/10.48550/arXiv.2205.11991</a>","ieee":"D. Zikelic, M. Lechner, K. Chatterjee, and T. A. Henzinger, “Learning stabilizing policies in stochastic control systems,” <i>arXiv</i>. .","short":"D. Zikelic, M. Lechner, K. Chatterjee, T.A. Henzinger, ArXiv (n.d.)."},"external_id":{"arxiv":["2205.11991"]},"oa_version":"Preprint","ec_funded":1,"status":"public","date_published":"2022-05-24T00:00:00Z","type":"preprint","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"oa":1,"month":"05","publication":"arXiv","_id":"14601","title":"Learning stabilizing policies in stochastic control systems","doi":"10.48550/arXiv.2205.11991","date_updated":"2025-07-14T09:10:00Z","abstract":[{"text":"In this work, we address the problem of learning provably stable neural\r\nnetwork policies for stochastic control systems. While recent work has\r\ndemonstrated the feasibility of certifying given policies using martingale\r\ntheory, the problem of how to learn such policies is little explored. Here, we\r\nstudy the effectiveness of jointly learning a policy together with a martingale\r\ncertificate that proves its stability using a single learning algorithm. We\r\nobserve that the joint optimization problem becomes easily stuck in local\r\nminima when starting from a randomly initialized policy. Our results suggest\r\nthat some form of pre-training of the policy is required for the joint\r\noptimization to repair and verify the policy successfully.","lang":"eng"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"submitted","day":"24","arxiv":1,"date_created":"2023-11-24T13:22:30Z","author":[{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"language":[{"iso":"eng"}],"year":"2022","related_material":{"record":[{"id":"14539","relation":"dissertation_contains","status":"public"}]}},{"status":"public","intvolume":"        14","citation":{"ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859.","apa":"Friml, J. (2022). Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/cshperspect.a039859 \">https://doi.org/10.1101/cshperspect.a039859 </a>","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","ieee":"J. Friml, “Fourteen stations of auxin,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory, 2022.","ama":"Friml J. Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. 2022;14(5). doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859 \">10.1101/cshperspect.a039859 </a>","mla":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859 \">10.1101/cshperspect.a039859 </a>.","chicago":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/cshperspect.a039859 \">https://doi.org/10.1101/cshperspect.a039859 </a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039859 "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research. "}],"title":"Fourteen stations of auxin","_id":"10016","pmid":1,"acknowledgement":"The author thanks the whole community of researchers consciously or unconsciously working on questions related to auxin, whose hard work and enthusiasm contributed to development of this exciting story. Particular thanks go to many\r\nbrilliant present and past members of the Friml group and our numerous excellent collaborators, without whom my own personal journey would not be possible. The way of the cross with its 14 stations is a popular devotion among Roman Catholics and inspires them to make a spiritual pilgrimage through contemplation of Christ on his last day. Its aspects of gradual progress, struggle, passion, and revelation served as an inspiration for the formal depiction of our journey to understanding auxin as described in this review. It is in no way intended to reflect the personal beliefs of the author and readers. I am grateful to Nick Barton, Eva Benková, Lenka Caisová, Matyáš Fendrych, Lukáš Fiedler, Monika Frátriková, Jarmila Frimlová, Michelle Gallei, Jakub Hajný, Lukas Hoermayer, Alexandra Mally, Ondrˇej Novák, Jan Petrášek, Aleš Pěnčík, Steffen Vanneste, Tongda Xu, and Zhenbiao Yang for their valuable comments. Special thanks go to Michelle Gallei for her invaluable assistance with the figures.","issue":"5","publication_identifier":{"issn":["1943-0264"]},"scopus_import":"1","isi":1,"type":"journal_article","date_published":"2022-05-27T00:00:00Z","volume":14,"oa_version":"Published Version","external_id":{"pmid":["34400554"],"isi":["000806563000003"]},"article_type":"review","article_processing_charge":"No","doi":"10.1101/cshperspect.a039859 ","publisher":"Cold Spring Harbor Laboratory","date_updated":"2023-08-02T06:54:42Z","publication":"Cold Spring Harbor Perspectives in Biology","month":"05","oa":1,"quality_controlled":"1","article_number":"a039859","author":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"date_created":"2021-09-14T11:36:53Z","day":"27","publication_status":"published","language":[{"iso":"eng"}],"year":"2022","department":[{"_id":"JiFr"}]},{"oa_version":"Published Version","article_type":"original","external_id":{"arxiv":["2109.06778"],"isi":["000881319200001"]},"date_published":"2022-11-10T00:00:00Z","type":"journal_article","project":[{"call_identifier":"FWF","name":"New frontiers of the Manin conjecture","grant_number":"P32428","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"month":"11","publication":"Journal of the Institute of Mathematics of Jussieu","publisher":"Cambridge University Press","doi":"10.1017/S1474748022000482","date_updated":"2023-08-02T06:55:10Z","article_processing_charge":"Yes (via OA deal)","publication_status":"epub_ahead","day":"10","date_created":"2021-09-15T10:06:48Z","arxiv":1,"author":[{"last_name":"Derenthal","first_name":"Ulrich","full_name":"Derenthal, Ulrich"},{"last_name":"Wilsch","orcid":"0000-0001-7302-8256","first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander"}],"keyword":["Integral points","del Pezzo surface","universal torsor","Manin’s conjecture"],"department":[{"_id":"TiBr"}],"language":[{"iso":"eng"}],"year":"2022","main_file_link":[{"url":"https://doi.org/10.1017/S1474748022000482","open_access":"1"}],"citation":{"chicago":"Derenthal, Ulrich, and Florian Alexander Wilsch. “Integral Points on Singular Del Pezzo Surfaces.” <i>Journal of the Institute of Mathematics of Jussieu</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/S1474748022000482\">https://doi.org/10.1017/S1474748022000482</a>.","mla":"Derenthal, Ulrich, and Florian Alexander Wilsch. “Integral Points on Singular Del Pezzo Surfaces.” <i>Journal of the Institute of Mathematics of Jussieu</i>, Cambridge University Press, 2022, doi:<a href=\"https://doi.org/10.1017/S1474748022000482\">10.1017/S1474748022000482</a>.","ama":"Derenthal U, Wilsch FA. Integral points on singular del Pezzo surfaces. <i>Journal of the Institute of Mathematics of Jussieu</i>. 2022. doi:<a href=\"https://doi.org/10.1017/S1474748022000482\">10.1017/S1474748022000482</a>","ieee":"U. Derenthal and F. A. Wilsch, “Integral points on singular del Pezzo surfaces,” <i>Journal of the Institute of Mathematics of Jussieu</i>. Cambridge University Press, 2022.","short":"U. Derenthal, F.A. Wilsch, Journal of the Institute of Mathematics of Jussieu (2022).","apa":"Derenthal, U., &#38; Wilsch, F. A. (2022). Integral points on singular del Pezzo surfaces. <i>Journal of the Institute of Mathematics of Jussieu</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S1474748022000482\">https://doi.org/10.1017/S1474748022000482</a>","ista":"Derenthal U, Wilsch FA. 2022. Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu."},"status":"public","acknowledgement":"The first author was partly supported by grant DE 1646/4-2 of the Deutsche Forschungsgemeinschaft. The second author was partly supported by FWF grant P 32428-N35 and conducted part of this work as a guest at the Institut de Mathématiques de Jussieu–Paris Rive Gauche invited by Antoine Chambert-Loir and funded by DAAD.","_id":"10018","title":"Integral points on singular del Pezzo surfaces","abstract":[{"lang":"eng","text":"In order to study integral points of bounded log-anticanonical height on weak del Pezzo surfaces, we classify weak del Pezzo pairs. As a representative example, we consider a quartic del Pezzo surface of singularity type A1 + A3 and prove an analogue of Manin's conjecture for integral points with respect to its singularities and its lines."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["1474-7480"],"eissn":["1475-3030 "]},"isi":1,"scopus_import":"1"},{"type":"journal_article","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"}],"date_published":"2022-01-25T00:00:00Z","volume":16,"article_type":"original","external_id":{"pmid":["34549956"],"isi":["000767223400008"]},"oa_version":"Published Version","doi":"10.1021/acsnano.1c06720","date_updated":"2023-08-02T14:41:05Z","publisher":"American Chemical Society ","publication":"ACS Nano","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","file":[{"file_size":9050764,"date_updated":"2022-03-02T16:17:29Z","checksum":"74f9c1aa5f95c0b992a4328e8e0247b4","file_name":"2022_ACSNano_Liu.pdf","access_level":"open_access","success":1,"creator":"cchlebak","relation":"main_file","file_id":"10808","date_created":"2022-03-02T16:17:29Z","content_type":"application/pdf"}],"oa":1,"month":"01","page":"78-88","keyword":["tin selenide","nanocomposite","grain growth","Zener pinning","thermoelectricity","annealing","solution processing"],"author":[{"orcid":"0000-0001-7313-6740","last_name":"Liu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"},{"full_name":"Yu, Yuan","first_name":"Yuan","last_name":"Yu"},{"first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee"},{"last_name":"Chang","orcid":"0000-0002-9515-4277","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng"},{"full_name":"David, Jérémy","first_name":"Jérémy","last_name":"David"},{"last_name":"Ghosh","full_name":"Ghosh, Tanmoy","id":"a5fc9bc3-feff-11ea-93fe-e8015a3c7e9d","first_name":"Tanmoy"},{"first_name":"Maria Chiara","full_name":"Spadaro, Maria Chiara","last_name":"Spadaro"},{"last_name":"Xie","first_name":"Chenyang","full_name":"Xie, Chenyang"},{"last_name":"Cojocaru-Mirédin","full_name":"Cojocaru-Mirédin, Oana","first_name":"Oana"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"day":"25","publication_status":"published","date_created":"2021-09-24T07:55:12Z","related_material":{"record":[{"id":"12885","status":"public","relation":"dissertation_contains"}]},"year":"2022","ddc":["540"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"MaIb"}],"status":"public","ec_funded":1,"intvolume":"        16","citation":{"ama":"Liu Y, Calcabrini M, Yu Y, et al. Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. <i>ACS Nano</i>. 2022;16(1):78-88. doi:<a href=\"https://doi.org/10.1021/acsnano.1c06720\">10.1021/acsnano.1c06720</a>","mla":"Liu, Yu, et al. “Defect Engineering in Solution-Processed Polycrystalline SnSe Leads to High Thermoelectric Performance.” <i>ACS Nano</i>, vol. 16, no. 1, American Chemical Society , 2022, pp. 78–88, doi:<a href=\"https://doi.org/10.1021/acsnano.1c06720\">10.1021/acsnano.1c06720</a>.","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Seungho Lee, Cheng Chang, Jérémy David, Tanmoy Ghosh, et al. “Defect Engineering in Solution-Processed Polycrystalline SnSe Leads to High Thermoelectric Performance.” <i>ACS Nano</i>. American Chemical Society , 2022. <a href=\"https://doi.org/10.1021/acsnano.1c06720\">https://doi.org/10.1021/acsnano.1c06720</a>.","ista":"Liu Y, Calcabrini M, Yu Y, Lee S, Chang C, David J, Ghosh T, Spadaro MC, Xie C, Cojocaru-Mirédin O, Arbiol J, Ibáñez M. 2022. Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. ACS Nano. 16(1), 78–88.","apa":"Liu, Y., Calcabrini, M., Yu, Y., Lee, S., Chang, C., David, J., … Ibáñez, M. (2022). Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. <i>ACS Nano</i>. American Chemical Society . <a href=\"https://doi.org/10.1021/acsnano.1c06720\">https://doi.org/10.1021/acsnano.1c06720</a>","ieee":"Y. Liu <i>et al.</i>, “Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance,” <i>ACS Nano</i>, vol. 16, no. 1. American Chemical Society , pp. 78–88, 2022.","short":"Y. Liu, M. Calcabrini, Y. Yu, S. Lee, C. Chang, J. David, T. Ghosh, M.C. Spadaro, C. Xie, O. Cojocaru-Mirédin, J. Arbiol, M. Ibáñez, ACS Nano 16 (2022) 78–88."},"has_accepted_license":"1","title":"Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance","_id":"10042","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"SnSe has emerged as one of the most promising materials for thermoelectric energy conversion due to its extraordinary performance in its single-crystal form and its low-cost constituent elements. However, to achieve an economic impact, the polycrystalline counterpart needs to replicate the performance of the single crystal. Herein, we optimize the thermoelectric performance of polycrystalline SnSe produced by consolidating solution-processed and surface-engineered SnSe particles. In particular, the SnSe particles are coated with CdSe molecular complexes that crystallize during the sintering process, forming CdSe nanoparticles. The presence of CdSe nanoparticles inhibits SnSe grain growth during the consolidation step due to Zener pinning, yielding a material with a high density of grain boundaries. Moreover, the resulting SnSe–CdSe nanocomposites present a large number of defects at different length scales, which significantly reduce the thermal conductivity. The produced SnSe–CdSe nanocomposites exhibit thermoelectric figures of merit up to 2.2 at 786 K, which is among the highest reported for solution-processed SnSe."}],"acknowledgement":"This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. S.L. and M.C. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. J.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 665919 (P-SPHERE) cofunded by Severo Ochoa Programme. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. M.C.S. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754510 (PROBIST) and the Severo Ochoa programme. J.D. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 665919 (P-SPHERE) cofunded by Severo Ochoa Programme. The ICN2 is funded by the CERCA Program/Generalitat de Catalunya and by the Severo Ochoa program of the Spanish Ministry of Economy, Industry, and Competitiveness (MINECO, grant no. SEV-2017-0706). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). This project received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 823717-ESTEEM3. The FIB sample preparation was conducted in the LMA-INA-Universidad de Zaragoza.","pmid":1,"issue":"1","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"scopus_import":"1","isi":1,"file_date_updated":"2022-03-02T16:17:29Z"},{"scopus_import":"1","isi":1,"publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"title":"The assembly, regulation and function of the mitochondrial respiratory chain","_id":"10182","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases."}],"pmid":1,"status":"public","intvolume":"        23","citation":{"chicago":"Vercellino, Irene, and Leonid A Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41580-021-00415-0\">https://doi.org/10.1038/s41580-021-00415-0</a>.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 23, Springer Nature, 2022, pp. 141–161, doi:<a href=\"https://doi.org/10.1038/s41580-021-00415-0\">10.1038/s41580-021-00415-0</a>.","ama":"Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. <i>Nature Reviews Molecular Cell Biology</i>. 2022;23:141–161. doi:<a href=\"https://doi.org/10.1038/s41580-021-00415-0\">10.1038/s41580-021-00415-0</a>","ieee":"I. Vercellino and L. A. Sazanov, “The assembly, regulation and function of the mitochondrial respiratory chain,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 23. Springer Nature, pp. 141–161, 2022.","short":"I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022) 141–161.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2022). The assembly, regulation and function of the mitochondrial respiratory chain. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-021-00415-0\">https://doi.org/10.1038/s41580-021-00415-0</a>","ista":"Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161."},"language":[{"iso":"eng"}],"year":"2022","department":[{"_id":"LeSa"}],"page":"141–161","author":[{"last_name":"Vercellino","orcid":" 0000-0001-5618-3449","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"day":"01","publication_status":"published","date_created":"2021-10-24T22:01:35Z","publisher":"Springer Nature","doi":"10.1038/s41580-021-00415-0","date_updated":"2023-08-02T06:55:42Z","publication":"Nature Reviews Molecular Cell Biology","article_processing_charge":"No","quality_controlled":"1","month":"02","type":"journal_article","date_published":"2022-02-01T00:00:00Z","volume":23,"article_type":"original","oa_version":"None","external_id":{"pmid":["34621061"],"isi":["000705697100001"]}},{"publication_identifier":{"eissn":["1868-5145"],"issn":["1868-5137"]},"file_date_updated":"2022-12-20T23:30:08Z","isi":1,"scopus_import":"1","has_accepted_license":"1","citation":{"chicago":"Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>.","mla":"Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>.","ama":"Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. 2022;13:2621–2635. doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>","ieee":"S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13. Springer Nature, pp. 2621–2635, 2022.","short":"S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635.","apa":"Goudarzi, S., Sharif, M., &#38; Karimipour, F. (2022). A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>","ista":"Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 13, 2621–2635."},"intvolume":"        13","status":"public","acknowledgement":"The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","_id":"10208","title":"A context-aware dimension reduction framework for trajectory and health signal analyses","abstract":[{"text":"It is practical to collect a huge amount of movement data and environmental context information along with the health signals of individuals because there is the emergence of new generations of positioning and tracking technologies and rapid advancements of health sensors. The study of the relations between these datasets and their sequence similarity analysis is of interest to many applications such as health monitoring and recommender systems. However, entering all movement parameters and health signals can lead to the complexity of the problem and an increase in its computational load. In this situation, dimension reduction techniques can be used to avoid consideration of simultaneous dependent parameters in the process of similarity measurement of the trajectories. The present study provides a framework, named CaDRAW, to use spatial–temporal data and movement parameters along with independent context information in the process of measuring the similarity of trajectories. In this regard, the omission of dependent movement characteristic signals is conducted by using an unsupervised feature selection dimension reduction technique. To evaluate the effectiveness of the proposed framework, it was applied to a real contextualized movement and related health signal datasets of individuals. The results indicated the capability of the proposed framework in measuring the similarity and in decreasing the characteristic signals in such a way that the similarity results -before and after reduction of dependent characteristic signals- have small differences. The mean differences between the obtained results before and after reducing the dimension were 0.029 and 0.023 for the round path, respectively.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","day":"01","date_created":"2021-11-02T09:28:55Z","page":"2621–2635","keyword":["general computer science"],"author":[{"first_name":"Samira","full_name":"Goudarzi, Samira","last_name":"Goudarzi"},{"last_name":"Sharif","full_name":"Sharif, Mohammad","first_name":"Mohammad"},{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","full_name":"Karimipour, Farid","last_name":"Karimipour","orcid":"0000-0001-6746-4174"}],"department":[{"_id":"HeEd"}],"ddc":["000"],"language":[{"iso":"eng"}],"year":"2022","oa_version":"Submitted Version","article_type":"original","external_id":{"isi":["000712198000001"]},"volume":13,"type":"journal_article","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"}],"date_published":"2022-05-01T00:00:00Z","oa":1,"quality_controlled":"1","file":[{"date_updated":"2022-12-20T23:30:08Z","file_size":1634958,"access_level":"open_access","file_name":"A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf","checksum":"0a8961416a9bb2be5a1cebda65468bcf","relation":"main_file","creator":"fkarimip","content_type":"application/pdf","date_created":"2021-11-12T19:38:05Z","file_id":"10279","embargo":"2022-11-12"}],"month":"05","publication":"Journal of Ambient Intelligence and Humanized Computing","publisher":"Springer Nature","date_updated":"2023-08-02T13:31:48Z","doi":"10.1007/s12652-021-03569-z","article_processing_charge":"No"},{"isi":1,"scopus_import":"1","file_date_updated":"2022-02-03T13:37:11Z","issue":"1","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"_id":"10284","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","abstract":[{"lang":"eng","text":"Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing ‘superorganisms’––incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"The authors are grateful to G. Tkačik and V. Mireles for advice on data analyses and to A. Schloegl for help using the IST Austria HPC cluster for data processing. The authors thank J. Eilenberg for providing the fungal strain and A.V. Grasse for support with the molecular analysis. The authors also thank the Social Immunity group at IST Austria, in particular B. Milutinović, for discussions throughout and comments on the manuscript.","pmid":1,"ec_funded":1,"status":"public","has_accepted_license":"1","intvolume":"        25","citation":{"chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>.","mla":"Casillas Perez, Barbara E., et al. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>, vol. 25, no. 1, Wiley, 2022, pp. 89–100, doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. 2022;25(1):89-100. doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100.","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies,” <i>Ecology Letters</i>, vol. 25, no. 1. Wiley, pp. 89–100, 2022.","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &#38; Cremer, S. (2022). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2022. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. 25(1), 89–100."},"year":"2022","ddc":["573"],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13061"}]},"department":[{"_id":"SyCr"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"page":"89-100","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","full_name":"Pull, Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982"},{"last_name":"Naiser","first_name":"Filip","full_name":"Naiser, Filip"},{"full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger"},{"first_name":"Jiri","full_name":"Matas, Jiri","last_name":"Matas"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publication_status":"published","day":"01","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2021-11-14T23:01:25Z","publication":"Ecology Letters","doi":"10.1111/ele.13907","date_updated":"2023-08-14T11:45:29Z","publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","file":[{"creator":"cchlebak","relation":"main_file","file_id":"10721","date_created":"2022-02-03T13:37:11Z","content_type":"application/pdf","file_size":700087,"date_updated":"2022-02-03T13:37:11Z","checksum":"0bd4210400e9876609b7c538ab4f9a3c","access_level":"open_access","file_name":"2021_EcologyLetters_CasillasPerez.pdf","success":1}],"oa":1,"month":"01","volume":25,"project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"type":"journal_article","date_published":"2022-01-01T00:00:00Z","oa_version":"Published Version","article_type":"original","external_id":{"pmid":["34725912"],"isi":["000713396100001"]}},{"language":[{"iso":"eng"}],"year":"2022","ddc":["514","516"],"department":[{"_id":"UlWa"}],"page":"1317-1345","author":[{"orcid":"0000-0002-2512-8698","last_name":"Kaluza","first_name":"Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","full_name":"Kaluza, Vojtech"},{"full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer"}],"publication_status":"published","day":"01","arxiv":1,"date_created":"2021-11-25T13:49:16Z","publication":"Combinatorica","date_updated":"2023-08-02T06:43:27Z","publisher":"Springer Nature","doi":"10.1007/s00493-021-4443-7","article_processing_charge":"No","quality_controlled":"1","oa":1,"month":"12","volume":42,"date_published":"2022-12-01T00:00:00Z","type":"journal_article","external_id":{"isi":["000798210100003"],"arxiv":["1907.05055"]},"oa_version":"Preprint","article_type":"original","isi":1,"scopus_import":"1","publication_identifier":{"issn":["0209-9683"]},"_id":"10335","title":"Even maps, the Colin de Verdière number and representations of graphs","abstract":[{"lang":"eng","text":"Van der Holst and Pendavingh introduced a graph parameter σ, which coincides with the more famous Colin de Verdière graph parameter μ for small values. However, the definition of a is much more geometric/topological directly reflecting embeddability properties of the graph. They proved μ(G) ≤ σ(G) + 2 and conjectured σ(G) ≤ σ(G) for any graph G. We confirm this conjecture. As far as we know, this is the first topological upper bound on σ(G) which is, in general, tight.\r\nEquality between μ and σ does not hold in general as van der Holst and Pendavingh showed that there is a graph G with μ(G) ≤ 18 and σ(G) ≥ 20. We show that the gap appears at much smaller values, namely, we exhibit a graph H for which μ(H) ≥ 7 and σ(H) ≥ 8. We also prove that, in general, the gap can be large: The incidence graphs Hq of finite projective planes of order q satisfy μ(Hq) ∈ O(q3/2) and σ(Hq) ≥ q2."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"V. K. gratefully acknowledges the support of Austrian Science Fund (FWF): P 30902-N35. This work was done mostly while he was employed at the University of Innsbruck. During the early stage of this research, V. K. was partially supported by Charles University project GAUK 926416. M. T. is supported by the grant no. 19-04113Y of the Czech Science Foundation(GA ˇCR) and partially supported by Charles University project UNCE/SCI/004.","status":"public","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1907.05055","open_access":"1"}],"intvolume":"        42","citation":{"mla":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” <i>Combinatorica</i>, vol. 42, Springer Nature, 2022, pp. 1317–45, doi:<a href=\"https://doi.org/10.1007/s00493-021-4443-7\">10.1007/s00493-021-4443-7</a>.","ama":"Kaluza V, Tancer M. Even maps, the Colin de Verdière number and representations of graphs. <i>Combinatorica</i>. 2022;42:1317-1345. doi:<a href=\"https://doi.org/10.1007/s00493-021-4443-7\">10.1007/s00493-021-4443-7</a>","chicago":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” <i>Combinatorica</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00493-021-4443-7\">https://doi.org/10.1007/s00493-021-4443-7</a>.","apa":"Kaluza, V., &#38; Tancer, M. (2022). Even maps, the Colin de Verdière number and representations of graphs. <i>Combinatorica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00493-021-4443-7\">https://doi.org/10.1007/s00493-021-4443-7</a>","ista":"Kaluza V, Tancer M. 2022. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 42, 1317–1345.","short":"V. Kaluza, M. Tancer, Combinatorica 42 (2022) 1317–1345.","ieee":"V. Kaluza and M. Tancer, “Even maps, the Colin de Verdière number and representations of graphs,” <i>Combinatorica</i>, vol. 42. Springer Nature, pp. 1317–1345, 2022."}},{"acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC) and by Huawei. M. Mondelli is partially\r\nsupported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by\r\nthe National Science Foundation under Grant CCF-1764104.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1-1/μ + N/P log2 log2 N/P), where N is the block length of the code and μ is the scaling exponent of the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P = N/2, the latency of SSC decoding is O(N1-1/μ), which is sublinear in the block length. This recovers a result from our earlier work. Second, in a fully-serial implementation where P = 1, the latency of SSC decoding scales as O(N log2 log2 N). The multiplicative constant is also calculated: we show that the latency of SSC decoding when P = 1 is given by (2 + o(1))N log2 log2 N. Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P = N1/μ. The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations.","lang":"eng"}],"title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","_id":"10364","intvolume":"        21","citation":{"ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2022;21(6):3909-3920. doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6, Institute of Electrical and Electronics Engineers, 2022, pp. 3909–20, doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>.","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>.","ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2022. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 21(6), 3909–3920.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., &#38; Goldsmith, A. (2022). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>","short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.","ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6. Institute of Electrical and Electronics Engineers, pp. 3909–3920, 2022."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.13378"}],"status":"public","scopus_import":"1","isi":1,"publication_identifier":{"eissn":["1558-2248"],"issn":["1536-1276"]},"issue":"6","month":"06","quality_controlled":"1","oa":1,"article_processing_charge":"No","publisher":"Institute of Electrical and Electronics Engineers","date_updated":"2024-09-10T13:03:18Z","doi":"10.1109/TWC.2021.3125626","publication":"IEEE Transactions on Wireless Communications","oa_version":"Preprint","article_type":"original","external_id":{"isi":["000809406400028"],"arxiv":["2012.13378"]},"type":"journal_article","date_published":"2022-06-01T00:00:00Z","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"volume":21,"department":[{"_id":"MaMo"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10053"}]},"language":[{"iso":"eng"}],"year":"2022","date_created":"2021-11-28T23:01:29Z","arxiv":1,"day":"01","publication_status":"published","author":[{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco"},{"last_name":"Fazeli","full_name":"Fazeli, Arman","first_name":"Arman"},{"first_name":"Alexander","full_name":"Vardy, Alexander","last_name":"Vardy"},{"first_name":"John","full_name":"Cioffi, John","last_name":"Cioffi"},{"last_name":"Goldsmith","full_name":"Goldsmith, Andrea","first_name":"Andrea"}],"page":"3909-3920"},{"publication_identifier":{"issn":["1360-1385"]},"issue":"5","file_date_updated":"2023-11-02T17:00:03Z","scopus_import":"1","isi":1,"intvolume":"        27","citation":{"ista":"Li L, Gallei MC, Friml J. 2022. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 27(5), 440–449.","apa":"Li, L., Gallei, M. C., &#38; Friml, J. (2022). Bending to auxin: Fast acid growth for tropisms. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">https://doi.org/10.1016/j.tplants.2021.11.006</a>","short":"L. Li, M.C. Gallei, J. Friml, Trends in Plant Science 27 (2022) 440–449.","ieee":"L. Li, M. C. Gallei, and J. Friml, “Bending to auxin: Fast acid growth for tropisms,” <i>Trends in Plant Science</i>, vol. 27, no. 5. Cell Press, pp. 440–449, 2022.","ama":"Li L, Gallei MC, Friml J. Bending to auxin: Fast acid growth for tropisms. <i>Trends in Plant Science</i>. 2022;27(5):440-449. doi:<a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">10.1016/j.tplants.2021.11.006</a>","mla":"Li, Lanxin, et al. “Bending to Auxin: Fast Acid Growth for Tropisms.” <i>Trends in Plant Science</i>, vol. 27, no. 5, Cell Press, 2022, pp. 440–49, doi:<a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">10.1016/j.tplants.2021.11.006</a>.","chicago":"Li, Lanxin, Michelle C Gallei, and Jiří Friml. “Bending to Auxin: Fast Acid Growth for Tropisms.” <i>Trends in Plant Science</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">https://doi.org/10.1016/j.tplants.2021.11.006</a>."},"has_accepted_license":"1","status":"public","acknowledgement":"The authors thank Alexandra Mally for editing the text. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 to Jiří Friml and the DOC Fellowship of the Austrian Academy of Sciences to Lanxin Li. All figures were created with BioRender.com.","pmid":1,"title":"Bending to auxin: Fast acid growth for tropisms","_id":"10411","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The phytohormone auxin is the major growth regulator governing tropic responses including gravitropism. Auxin build-up at the lower side of stimulated shoots promotes cell expansion, whereas in roots it inhibits growth, leading to upward shoot bending and downward root bending, respectively. Yet it remains an enigma how the same signal can trigger such opposite cellular responses. In this review, we discuss several recent unexpected insights into the mechanisms underlying auxin regulation of growth, challenging several existing models. We focus on the divergent mechanisms of apoplastic pH regulation in shoots and roots revisiting the classical Acid Growth Theory and discuss coordinated involvement of multiple auxin signaling pathways. From this emerges a more comprehensive, updated picture how auxin regulates growth.","lang":"eng"}],"day":"01","publication_status":"published","date_created":"2021-12-05T23:01:43Z","page":"440-449","author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X"},{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"department":[{"_id":"JiFr"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"ddc":["580"],"language":[{"iso":"eng"}],"year":"2022","oa_version":"Submitted Version","article_type":"original","external_id":{"isi":["000793707900005"],"pmid":["34848141"]},"project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"type":"journal_article","date_published":"2022-05-01T00:00:00Z","volume":27,"file":[{"date_created":"2023-11-02T17:00:03Z","file_id":"14480","content_type":"application/pdf","creator":"amally","relation":"main_file","checksum":"3d94980ee1ff6bec100dd813f6a921a6","success":1,"file_name":"Li Plants 2021_accepted.pdf","access_level":"open_access","file_size":805779,"date_updated":"2023-11-02T17:00:03Z"}],"quality_controlled":"1","oa":1,"month":"05","publisher":"Cell Press","date_updated":"2024-10-29T10:12:33Z","doi":"10.1016/j.tplants.2021.11.006","publication":"Trends in Plant Science","article_processing_charge":"No"},{"status":"public","intvolume":"       309","citation":{"short":"D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology and Its Applications 309 (2022).","ieee":"D. Dikranjan, A. Giordano Bruno, H. P. Künzi, N. Zava, and D. Toller, “Generalized quasi-metric semilattices,” <i>Topology and its Applications</i>, vol. 309. Elsevier, 2022.","apa":"Dikranjan, D., Giordano Bruno, A., Künzi, H. P., Zava, N., &#38; Toller, D. (2022). Generalized quasi-metric semilattices. <i>Topology and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.topol.2021.107916\">https://doi.org/10.1016/j.topol.2021.107916</a>","ista":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized quasi-metric semilattices. Topology and its Applications. 309, 107916.","chicago":"Dikranjan, Dikran, Anna Giordano Bruno, Hans Peter Künzi, Nicolò Zava, and Daniele Toller. “Generalized Quasi-Metric Semilattices.” <i>Topology and Its Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.topol.2021.107916\">https://doi.org/10.1016/j.topol.2021.107916</a>.","mla":"Dikranjan, Dikran, et al. “Generalized Quasi-Metric Semilattices.” <i>Topology and Its Applications</i>, vol. 309, 107916, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.topol.2021.107916\">10.1016/j.topol.2021.107916</a>.","ama":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. Generalized quasi-metric semilattices. <i>Topology and its Applications</i>. 2022;309. doi:<a href=\"https://doi.org/10.1016/j.topol.2021.107916\">10.1016/j.topol.2021.107916</a>"},"abstract":[{"text":"Motivated by the recent introduction of the intrinsic semilattice entropy, we study generalized quasi-metric semilattices and their categories. We investigate the relationship between these objects and generalized semivaluations, extending Nakamura and Schellekens' approach. Finally, we use this correspondence to compare the intrinsic semilattice entropy and the semigroup entropy induced in particular situations, like sets, torsion abelian groups and vector spaces.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10413","title":"Generalized quasi-metric semilattices","acknowledgement":"Dedicated to the memory of Hans-Peter Künzi.","publication_identifier":{"issn":["0166-8641"]},"isi":1,"scopus_import":"1","volume":309,"date_published":"2022-03-15T00:00:00Z","type":"journal_article","external_id":{"isi":["000791838800012"]},"oa_version":"None","article_type":"original","article_processing_charge":"No","publication":"Topology and its Applications","date_updated":"2023-08-02T13:33:24Z","publisher":"Elsevier","doi":"10.1016/j.topol.2021.107916","month":"03","article_number":"107916","quality_controlled":"1","author":[{"full_name":"Dikranjan, Dikran","first_name":"Dikran","last_name":"Dikranjan"},{"first_name":"Anna","full_name":"Giordano Bruno, Anna","last_name":"Giordano Bruno"},{"last_name":"Künzi","first_name":"Hans Peter","full_name":"Künzi, Hans Peter"},{"full_name":"Zava, Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","first_name":"Nicolò","orcid":"0000-0001-8686-1888","last_name":"Zava"},{"full_name":"Toller, Daniele","first_name":"Daniele","last_name":"Toller"}],"date_created":"2021-12-05T23:01:44Z","publication_status":"published","day":"15","language":[{"iso":"eng"}],"year":"2022","department":[{"_id":"HeEd"}]},{"acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","_id":"10530","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"intvolume":"       121","citation":{"ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>."},"has_accepted_license":"1","status":"public","file_date_updated":"2022-07-29T10:17:10Z","isi":1,"publication_identifier":{"issn":["0006-3495"]},"issue":"1","file":[{"file_size":4475504,"date_updated":"2022-07-29T10:17:10Z","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","success":1,"access_level":"open_access","file_name":"2022_BiophysicalJour_Zisis.pdf","relation":"main_file","creator":"dernst","date_created":"2022-07-29T10:17:10Z","file_id":"11697","content_type":"application/pdf"}],"oa":1,"quality_controlled":"1","month":"01","publisher":"Elsevier","doi":"10.1016/j.bpj.2021.12.006","date_updated":"2023-08-02T13:34:25Z","publication":"Biophysical Journal","article_processing_charge":"No","external_id":{"isi":["000740815400007"]},"oa_version":"Published Version","article_type":"original","type":"journal_article","date_published":"2022-01-04T00:00:00Z","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"volume":121,"department":[{"_id":"EdHa"},{"_id":"GaTk"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"language":[{"iso":"eng"}],"ddc":["570"],"year":"2022","day":"04","publication_status":"published","date_created":"2021-12-10T09:48:19Z","page":"P44-60","author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"first_name":"Wei Xiong","full_name":"Siow, Wei Xiong","last_name":"Siow"},{"full_name":"d’Alessandro, Joseph","first_name":"Joseph","last_name":"d’Alessandro"},{"full_name":"Vollmar, Angelika M.","first_name":"Angelika M.","last_name":"Vollmar"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"keyword":["Biophysics"]},{"month":"01","quality_controlled":"1","oa":1,"article_processing_charge":"No","publication":"SIAM Journal on Mathematical Analysis","date_updated":"2023-08-02T13:37:03Z","doi":"10.1137/20M1387237","publisher":"Society for Industrial and Applied Mathematics","external_id":{"isi":["000762768000006"],"arxiv":["2012.03792 "]},"article_type":"original","oa_version":"Preprint","volume":54,"type":"journal_article","date_published":"2022-01-04T00:00:00Z","department":[{"_id":"JuFi"}],"language":[{"iso":"eng"}],"year":"2022","arxiv":1,"date_created":"2021-12-16T12:08:56Z","publication_status":"published","day":"04","keyword":["Energy-Reaction-Diffusion Systems","Cross Diffusion","Global-In-Time Existence of Weak/Renormalised Solutions","Entropy Method","Onsager System","Soret/Dufour Effect"],"author":[{"full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","last_name":"Fischer"},{"full_name":"Hopf, Katharina","first_name":"Katharina","last_name":"Hopf"},{"full_name":"Kniely, Michael","first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","orcid":"0000-0001-5645-4333"},{"full_name":"Mielke, Alexander","first_name":"Alexander","last_name":"Mielke"}],"page":"220-267","acknowledgement":"M.K. gratefully acknowledges the hospitality of WIAS Berlin, where a major part of the project was carried out. The research stay of M.K. at WIAS Berlin was funded by the Austrian Federal Ministry of Education, Science and Research through a research fellowship for graduates of a promotio sub auspiciis. The research of A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems” (Project no. 235221301), Subproject C05 “Effective models for materials and interfaces with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin Schrödinger Institute in Vienna, where some ideas for this work have been developed. The authors are grateful to two anonymous referees for several helpful comments, in particular for the short proof of estimate (2.7).","abstract":[{"text":"We establish global-in-time existence results for thermodynamically consistent reaction-(cross-)diffusion systems coupled to an equation describing heat transfer. Our main interest is to model species-dependent diffusivities,\r\nwhile at the same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal case lies in the intrinsic presence of cross-diffusion type phenomena like the Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic equilibria, a nonvanishing temperature gradient may drive a concentration flux even in a situation with constant concentrations; likewise, a nonvanishing concentration gradient may drive a heat flux even in a case of spatially constant temperature. We use time discretisation and regularisation techniques and derive a priori estimates based on a suitable entropy and the associated entropy production. Renormalised solutions are used in cases where non-integrable diffusion fluxes or reaction terms appear.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10547","title":"Global existence analysis of energy-reaction-diffusion systems","main_file_link":[{"url":"https://arxiv.org/abs/2012.03792","open_access":"1"}],"intvolume":"        54","citation":{"ama":"Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):220-267. doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>","mla":"Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>.","chicago":"Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>.","ista":"Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1), 220–267.","apa":"Fischer, J. L., Hopf, K., Kniely, M., &#38; Mielke, A. (2022). Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>","ieee":"J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis of energy-reaction-diffusion systems,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.","short":"J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical Analysis 54 (2022) 220–267."},"status":"public","isi":1,"scopus_import":"1","publication_identifier":{"issn":["0036-1410"]},"issue":"1"}]