--- _id: '14356' 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. article_processing_charge: No article_type: original author: - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Hillary M. full_name: Porter, Hillary M. last_name: Porter - first_name: Mahmoud full_name: Izadi, Mahmoud last_name: Izadi - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Yves full_name: Lacassie, Yves last_name: Lacassie - first_name: Jill A. full_name: Rosenfeld, Jill A. last_name: Rosenfeld - first_name: Saadullah full_name: Khan, Saadullah last_name: Khan - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Tayyiba A. full_name: Ali, Tayyiba A. last_name: Ali - first_name: Nazif full_name: Muhammad, Nazif last_name: Muhammad - first_name: Sher A. full_name: Khan, Sher A. last_name: Khan - first_name: Noor full_name: Muhammad, Noor last_name: Muhammad - first_name: Pengfei full_name: Liu, Pengfei last_name: Liu - first_name: Marie-Louise full_name: Haymon, Marie-Louise last_name: Haymon - first_name: Franz full_name: Rueschendorf, Franz last_name: Rueschendorf - first_name: Il-Keun full_name: Kong, Il-Keun last_name: Kong - first_name: Linda full_name: Schnapp, Linda last_name: Schnapp - first_name: Natasha full_name: Shur, Natasha last_name: Shur - first_name: Lynn full_name: Chorich, Lynn last_name: Chorich - first_name: Lawrence full_name: Layman, Lawrence last_name: Layman - first_name: Thomas full_name: Haaf, Thomas last_name: Haaf - first_name: Ehsan full_name: Pourkarimi, Ehsan last_name: Pourkarimi - first_name: Hyung-Goo full_name: Kim, Hyung-Goo last_name: Kim - first_name: Gaurav K. full_name: Varshney, Gaurav K. last_name: Varshney citation: 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. Human Mutation. 2022;43(10):1472-1489. doi:10.1002/humu.24435 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. Human Mutation. Wiley. https://doi.org/10.1002/humu.24435 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.” Human Mutation. Wiley, 2022. https://doi.org/10.1002/humu.24435. ieee: S.-J. Lin et al., “Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function,” Human Mutation, vol. 43, no. 10. Wiley, pp. 1472–1489, 2022. 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. 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.” Human Mutation, vol. 43, no. 10, Wiley, 2022, pp. 1472–89, doi:10.1002/humu.24435. 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. date_created: 2023-09-20T20:58:24Z date_published: 2022-10-01T00:00:00Z date_updated: 2023-09-25T08:54:14Z day: '01' ddc: - '570' doi: 10.1002/humu.24435 extern: '1' file: - access_level: open_access checksum: 74b01d4e4084b2f64c30ed32b18ee928 content_type: application/pdf creator: dernst date_created: 2023-09-25T08:52:54Z date_updated: 2023-09-25T08:52:54Z file_id: '14370' file_name: 2022_HumanMutation_Lin.pdf file_size: 12131312 relation: main_file success: 1 file_date_updated: 2023-09-25T08:52:54Z has_accepted_license: '1' intvolume: ' 43' issue: '10' keyword: - autosomal recessive - biallelic variants - C - elegans - translation initiation sites - tryptophanyl-tRNA synthetase 1 (WARS1) - WHEP domain - zebrafish language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1472-1489 publication: Human Mutation publication_identifier: issn: - 1059-7794 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2022' ... --- _id: '14357' abstract: - lang: eng 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.' article_processing_charge: No article_type: original author: - first_name: Nina full_name: Boegershausen, Nina last_name: Boegershausen - first_name: Hannah E. full_name: Krawczyk, Hannah E. last_name: Krawczyk - first_name: Rami A. full_name: Jamra, Rami A. last_name: Jamra - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Goekhan full_name: Yigit, Goekhan last_name: Yigit - 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 - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Julia full_name: Schmidt, Julia last_name: Schmidt - first_name: Janine full_name: Altmueller, Janine last_name: Altmueller - first_name: Johannes full_name: Luppe, Johannes last_name: Luppe - first_name: Konrad full_name: Platzer, Konrad last_name: Platzer - first_name: Beate B. full_name: Doergeloh, Beate B. last_name: Doergeloh - first_name: Andreas full_name: Busche, Andreas last_name: Busche - first_name: Saskia full_name: Biskup, Saskia last_name: Biskup - first_name: Marisa full_name: Mendes, I, Marisa last_name: Mendes, I - first_name: Desiree E. C. full_name: Smith, Desiree E. C. last_name: Smith - first_name: Gajja S. full_name: Salomons, Gajja S. last_name: Salomons - first_name: Arne full_name: Zibat, Arne last_name: Zibat - first_name: Eva full_name: Bueltmann, Eva last_name: Bueltmann - first_name: Peter full_name: Nuernberg, Peter last_name: Nuernberg - first_name: Malte full_name: Spielmann, Malte last_name: Spielmann - first_name: Johannes R. full_name: Lemke, Johannes R. last_name: Lemke - first_name: Yun full_name: Li, Yun last_name: Li - first_name: Martin full_name: Zenker, Martin last_name: Zenker - first_name: Gaurav K. full_name: Varshney, Gaurav K. last_name: Varshney - first_name: Hauke S. full_name: Hillen, Hauke S. last_name: Hillen - first_name: Christian P. full_name: Kratz, Christian P. last_name: Kratz - first_name: Bernd full_name: Wollnik, Bernd last_name: Wollnik citation: ama: 'Boegershausen N, Krawczyk HE, Jamra RA, et al. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 2022;43(10):1454-1471. doi:10.1002/humu.24430' 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. Human Mutation. Wiley. https://doi.org/10.1002/humu.24430' 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.” Human Mutation. Wiley, 2022. https://doi.org/10.1002/humu.24430.' ieee: 'N. Boegershausen et al., “WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly,” Human Mutation, vol. 43, no. 10. Wiley, pp. 1454–1471, 2022.' 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.' mla: 'Boegershausen, Nina, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” Human Mutation, vol. 43, no. 10, Wiley, 2022, pp. 1454–71, doi:10.1002/humu.24430.' 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. date_created: 2023-09-20T20:59:33Z date_published: 2022-10-01T00:00:00Z date_updated: 2023-09-25T08:43:06Z day: '01' ddc: - '570' doi: 10.1002/humu.24430 extern: '1' external_id: pmid: - '35790048' file: - access_level: open_access checksum: c31fc91e0445c35b9da83eb911a9b552 content_type: application/pdf creator: dernst date_created: 2023-09-25T08:41:23Z date_updated: 2023-09-25T08:41:23Z file_id: '14367' file_name: 2022_HumanMutation_Boegershausen.pdf file_size: 4863605 relation: main_file success: 1 file_date_updated: 2023-09-25T08:41:23Z has_accepted_license: '1' intvolume: ' 43' issue: '10' keyword: - aminoacylation - aminoacyl-tRNA synthetase - ARS - CRISPR - Cas9 - intellectual disability - microcephaly - SARS1 - tRNA - WARS1 - zebrafish language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1454-1471 pmid: 1 publication: Human Mutation publication_identifier: issn: - 1059-7794 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly' 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2022' ... --- _id: '14381' 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. article_processing_charge: No article_type: original author: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Wagner U. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). Bulletin de la Societe Mathematique de France. 2022;438:281-294. doi:10.24033/ast.1188 apa: Wagner, U. (2022). High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). Bulletin de La Societe Mathematique de France. Societe Mathematique de France. https://doi.org/10.24033/ast.1188 chicago: Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” Bulletin de La Societe Mathematique de France. Societe Mathematique de France, 2022. https://doi.org/10.24033/ast.1188. ieee: U. Wagner, “High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others),” Bulletin de la Societe Mathematique de France, vol. 438. Societe Mathematique de France, pp. 281–294, 2022. ista: Wagner U. 2022. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). Bulletin de la Societe Mathematique de France. 438, 281–294. mla: Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” Bulletin de La Societe Mathematique de France, vol. 438, Societe Mathematique de France, 2022, pp. 281–94, doi:10.24033/ast.1188. short: U. Wagner, Bulletin de La Societe Mathematique de France 438 (2022) 281–294. date_created: 2023-10-01T22:01:14Z date_published: 2022-01-01T00:00:00Z date_updated: 2023-10-03T08:04:03Z day: '01' department: - _id: UlWa doi: 10.24033/ast.1188 intvolume: ' 438' language: - iso: eng month: '01' oa_version: None page: 281-294 publication: Bulletin de la Societe Mathematique de France publication_identifier: eissn: - 2102-622X issn: - 0037-9484 publication_status: published publisher: Societe Mathematique de France quality_controlled: '1' scopus_import: '1' status: public title: High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 438 year: '2022' ... --- _id: '14437' abstract: - lang: eng 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. article_processing_charge: No article_type: letter_note author: - first_name: Hendrik full_name: Utzat, Hendrik last_name: Utzat - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Utzat H, Ibáñez M. Molecular engineering enables bright blue LEDs. Nature. 2022;612(7941):638-639. doi:10.1038/d41586-022-04447-0 apa: Utzat, H., & Ibáñez, M. (2022). Molecular engineering enables bright blue LEDs. Nature. Springer Nature. https://doi.org/10.1038/d41586-022-04447-0 chicago: Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” Nature. Springer Nature, 2022. https://doi.org/10.1038/d41586-022-04447-0. ieee: H. Utzat and M. Ibáñez, “Molecular engineering enables bright blue LEDs,” Nature, vol. 612, no. 7941. Springer Nature, pp. 638–639, 2022. ista: Utzat H, Ibáñez M. 2022. Molecular engineering enables bright blue LEDs. Nature. 612(7941), 638–639. mla: Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” Nature, vol. 612, no. 7941, Springer Nature, 2022, pp. 638–39, doi:10.1038/d41586-022-04447-0. short: H. Utzat, M. Ibáñez, Nature 612 (2022) 638–639. date_created: 2023-10-17T11:14:43Z date_published: 2022-12-21T00:00:00Z date_updated: 2023-10-18T06:26:30Z day: '21' department: - _id: MaIb doi: 10.1038/d41586-022-04447-0 external_id: pmid: - '36543947' intvolume: ' 612' issue: '7941' keyword: - Multidisciplinary language: - iso: eng month: '12' oa_version: None page: 638-639 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Molecular engineering enables bright blue LEDs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 612 year: '2022' ... --- _id: '14520' 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.' article_processing_charge: No author: - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:10.5281/ZENODO.8408897' apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. https://doi.org/10.5281/ZENODO.8408897' 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. https://doi.org/10.5281/ZENODO.8408897.' ieee: 'M. Zemlicka et al., “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.' 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, 10.5281/ZENODO.8408897.' mla: 'Zemlicka, Martin, et al. Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses. Zenodo, 2022, doi:10.5281/ZENODO.8408897.' short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022). date_created: 2023-11-13T08:09:10Z date_published: 2022-06-28T00:00:00Z date_updated: 2024-09-10T12:23:57Z day: '28' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.8408897 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.8408897 month: '06' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14517' relation: used_in_publication status: public status: public title: 'Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '14597' 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." article_processing_charge: No arxiv: 1 author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Alice full_name: Marveggio, Alice id: 25647992-AA84-11E9-9D75-8427E6697425 last_name: Marveggio citation: ama: Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv. doi:10.48550/ARXIV.2203.17143 apa: Fischer, J. L., & Marveggio, A. (n.d.). Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv. https://doi.org/10.48550/ARXIV.2203.17143 chicago: Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2203.17143. ieee: J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow,” arXiv. . ista: Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv, 10.48550/ARXIV.2203.17143. mla: Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” ArXiv, doi:10.48550/ARXIV.2203.17143. short: J.L. Fischer, A. Marveggio, ArXiv (n.d.). date_created: 2023-11-23T09:30:02Z date_published: 2022-03-31T00:00:00Z date_updated: 2023-11-30T13:25:02Z day: '31' department: - _id: JuFi doi: 10.48550/ARXIV.2203.17143 ec_funded: 1 external_id: arxiv: - '2203.17143' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2203.17143 month: '03' oa: 1 oa_version: Preprint project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: arXiv publication_status: submitted related_material: record: - id: '14587' relation: dissertation_contains status: public status: public title: Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '14600' abstract: - lang: eng 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. article_processing_charge: No arxiv: 1 author: - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv. doi:10.48550/ARXIV.2210.05308 apa: Zikelic, D., Lechner, M., Henzinger, T. A., & Chatterjee, K. (n.d.). Learning control policies for stochastic systems with reach-avoid guarantees. arXiv. https://doi.org/10.48550/ARXIV.2210.05308 chicago: Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2210.05308. ieee: D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” arXiv. . ista: Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv, 10.48550/ARXIV.2210.05308. mla: Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” ArXiv, doi:10.48550/ARXIV.2210.05308. short: D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, ArXiv (n.d.). date_created: 2023-11-24T13:10:09Z date_published: 2022-11-29T00:00:00Z date_updated: 2025-07-14T09:10:02Z day: '29' department: - _id: KrCh - _id: ToHe doi: 10.48550/ARXIV.2210.05308 ec_funded: 1 external_id: arxiv: - '2210.05308' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ main_file_link: - open_access: '1' url: https://arxiv.org/abs/2210.05308 month: '11' oa: 1 oa_version: Preprint project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: arXiv publication_status: submitted related_material: record: - id: '14539' relation: dissertation_contains status: public - id: '14830' relation: later_version status: public status: public title: Learning control policies for stochastic systems with reach-avoid guarantees tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '14601' abstract: - lang: eng 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." article_processing_charge: No arxiv: 1 author: - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv. doi:10.48550/arXiv.2205.11991 apa: Zikelic, D., Lechner, M., Chatterjee, K., & Henzinger, T. A. (n.d.). Learning stabilizing policies in stochastic control systems. arXiv. https://doi.org/10.48550/arXiv.2205.11991 chicago: Zikelic, Dorde, Mathias Lechner, Krishnendu Chatterjee, and Thomas A Henzinger. “Learning Stabilizing Policies in Stochastic Control Systems.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2205.11991. ieee: D. Zikelic, M. Lechner, K. Chatterjee, and T. A. Henzinger, “Learning stabilizing policies in stochastic control systems,” arXiv. . ista: Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv, 10.48550/arXiv.2205.11991. mla: Zikelic, Dorde, et al. “Learning Stabilizing Policies in Stochastic Control Systems.” ArXiv, doi:10.48550/arXiv.2205.11991. short: D. Zikelic, M. Lechner, K. Chatterjee, T.A. Henzinger, ArXiv (n.d.). date_created: 2023-11-24T13:22:30Z date_published: 2022-05-24T00:00:00Z date_updated: 2025-07-14T09:10:00Z day: '24' department: - _id: KrCh - _id: ToHe doi: 10.48550/arXiv.2205.11991 ec_funded: 1 external_id: arxiv: - '2205.11991' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2205.11991 month: '05' oa: 1 oa_version: Preprint project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: arXiv publication_status: submitted related_material: record: - id: '14539' relation: dissertation_contains status: public status: public title: Learning stabilizing policies in stochastic control systems type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '10016' 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. ' 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." article_number: a039859 article_processing_charge: No article_type: review author: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Friml J. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 2022;14(5). doi:10.1101/cshperspect.a039859 apa: Friml, J. (2022). Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a039859 chicago: Friml, Jiří. “Fourteen Stations of Auxin.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/cshperspect.a039859 . ieee: J. Friml, “Fourteen stations of auxin,” Cold Spring Harbor Perspectives in Biology, vol. 14, no. 5. Cold Spring Harbor Laboratory, 2022. ista: Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859. mla: Friml, Jiří. “Fourteen Stations of Auxin.” Cold Spring Harbor Perspectives in Biology, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory, 2022, doi:10.1101/cshperspect.a039859 . short: J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022). date_created: 2021-09-14T11:36:53Z date_published: 2022-05-27T00:00:00Z date_updated: 2023-08-02T06:54:42Z day: '27' department: - _id: JiFr doi: '10.1101/cshperspect.a039859 ' external_id: isi: - '000806563000003' pmid: - '34400554' intvolume: ' 14' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/cshperspect.a039859 ' month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Cold Spring Harbor Perspectives in Biology publication_identifier: issn: - 1943-0264 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: Fourteen stations of auxin type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2022' ... --- _id: '10018' 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. 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. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Ulrich full_name: Derenthal, Ulrich last_name: Derenthal - first_name: Florian Alexander full_name: Wilsch, Florian Alexander id: 560601DA-8D36-11E9-A136-7AC1E5697425 last_name: Wilsch orcid: 0000-0001-7302-8256 citation: ama: Derenthal U, Wilsch FA. Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu. 2022. doi:10.1017/S1474748022000482 apa: Derenthal, U., & Wilsch, F. A. (2022). Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu. Cambridge University Press. https://doi.org/10.1017/S1474748022000482 chicago: Derenthal, Ulrich, and Florian Alexander Wilsch. “Integral Points on Singular Del Pezzo Surfaces.” Journal of the Institute of Mathematics of Jussieu. Cambridge University Press, 2022. https://doi.org/10.1017/S1474748022000482. ieee: U. Derenthal and F. A. Wilsch, “Integral points on singular del Pezzo surfaces,” Journal of the Institute of Mathematics of Jussieu. Cambridge University Press, 2022. ista: Derenthal U, Wilsch FA. 2022. Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu. mla: Derenthal, Ulrich, and Florian Alexander Wilsch. “Integral Points on Singular Del Pezzo Surfaces.” Journal of the Institute of Mathematics of Jussieu, Cambridge University Press, 2022, doi:10.1017/S1474748022000482. short: U. Derenthal, F.A. Wilsch, Journal of the Institute of Mathematics of Jussieu (2022). date_created: 2021-09-15T10:06:48Z date_published: 2022-11-10T00:00:00Z date_updated: 2023-08-02T06:55:10Z day: '10' department: - _id: TiBr doi: 10.1017/S1474748022000482 external_id: arxiv: - '2109.06778' isi: - '000881319200001' isi: 1 keyword: - Integral points - del Pezzo surface - universal torsor - Manin’s conjecture language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/S1474748022000482 month: '11' oa: 1 oa_version: Published Version project: - _id: 26AEDAB2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P32428 name: New frontiers of the Manin conjecture publication: Journal of the Institute of Mathematics of Jussieu publication_identifier: eissn: - '1475-3030 ' issn: - 1474-7480 publication_status: epub_ahead publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Integral points on singular del Pezzo surfaces type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2022' ... --- _id: '10042' 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.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini - first_name: Yuan full_name: Yu, Yuan last_name: Yu - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Jérémy full_name: David, Jérémy last_name: David - first_name: Tanmoy full_name: Ghosh, Tanmoy id: a5fc9bc3-feff-11ea-93fe-e8015a3c7e9d last_name: Ghosh - first_name: Maria Chiara full_name: Spadaro, Maria Chiara last_name: Spadaro - first_name: Chenyang full_name: Xie, Chenyang last_name: Xie - first_name: Oana full_name: Cojocaru-Mirédin, Oana last_name: Cojocaru-Mirédin - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Liu Y, Calcabrini M, Yu Y, et al. Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. ACS Nano. 2022;16(1):78-88. doi:10.1021/acsnano.1c06720 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. ACS Nano. American Chemical Society . https://doi.org/10.1021/acsnano.1c06720 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.” ACS Nano. American Chemical Society , 2022. https://doi.org/10.1021/acsnano.1c06720. ieee: Y. Liu et al., “Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance,” ACS Nano, vol. 16, no. 1. American Chemical Society , pp. 78–88, 2022. 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. mla: Liu, Yu, et al. “Defect Engineering in Solution-Processed Polycrystalline SnSe Leads to High Thermoelectric Performance.” ACS Nano, vol. 16, no. 1, American Chemical Society , 2022, pp. 78–88, doi:10.1021/acsnano.1c06720. 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. date_created: 2021-09-24T07:55:12Z date_published: 2022-01-25T00:00:00Z date_updated: 2023-08-02T14:41:05Z day: '25' ddc: - '540' department: - _id: MaIb doi: 10.1021/acsnano.1c06720 ec_funded: 1 external_id: isi: - '000767223400008' pmid: - '34549956' file: - access_level: open_access checksum: 74f9c1aa5f95c0b992a4328e8e0247b4 content_type: application/pdf creator: cchlebak date_created: 2022-03-02T16:17:29Z date_updated: 2022-03-02T16:17:29Z file_id: '10808' file_name: 2022_ACSNano_Liu.pdf file_size: 9050764 relation: main_file success: 1 file_date_updated: 2022-03-02T16:17:29Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '1' keyword: - tin selenide - nanocomposite - grain growth - Zener pinning - thermoelectricity - annealing - solution processing language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 78-88 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: 'American Chemical Society ' quality_controlled: '1' related_material: record: - id: '12885' relation: dissertation_contains status: public scopus_import: '1' status: public title: Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2022' ... --- _id: '10182' 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. article_processing_charge: No article_type: original author: - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: ' 0000-0001-5618-3449' - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 2022;23:141–161. doi:10.1038/s41580-021-00415-0 apa: Vercellino, I., & Sazanov, L. A. (2022). The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-021-00415-0 chicago: Vercellino, Irene, and Leonid A Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” Nature Reviews Molecular Cell Biology. Springer Nature, 2022. https://doi.org/10.1038/s41580-021-00415-0. ieee: I. Vercellino and L. A. Sazanov, “The assembly, regulation and function of the mitochondrial respiratory chain,” Nature Reviews Molecular Cell Biology, vol. 23. Springer Nature, pp. 141–161, 2022. ista: Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161. mla: Vercellino, Irene, and Leonid A. Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” Nature Reviews Molecular Cell Biology, vol. 23, Springer Nature, 2022, pp. 141–161, doi:10.1038/s41580-021-00415-0. short: I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022) 141–161. date_created: 2021-10-24T22:01:35Z date_published: 2022-02-01T00:00:00Z date_updated: 2023-08-02T06:55:42Z day: '01' department: - _id: LeSa doi: 10.1038/s41580-021-00415-0 external_id: isi: - '000705697100001' pmid: - '34621061' intvolume: ' 23' isi: 1 language: - iso: eng month: '02' oa_version: None page: 141–161 pmid: 1 publication: Nature Reviews Molecular Cell Biology publication_identifier: eissn: - 1471-0080 issn: - 1471-0072 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The assembly, regulation and function of the mitochondrial respiratory chain type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 23 year: '2022' ... --- _id: '10208' abstract: - lang: eng 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. acknowledgement: The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. article_processing_charge: No article_type: original author: - first_name: Samira full_name: Goudarzi, Samira last_name: Goudarzi - first_name: Mohammad full_name: Sharif, Mohammad last_name: Sharif - first_name: Farid full_name: Karimipour, Farid id: 2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425 last_name: Karimipour orcid: 0000-0001-6746-4174 citation: ama: Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 2022;13:2621–2635. doi:10.1007/s12652-021-03569-z apa: 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. Springer Nature. https://doi.org/10.1007/s12652-021-03569-z chicago: Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” Journal of Ambient Intelligence and Humanized Computing. Springer Nature, 2022. https://doi.org/10.1007/s12652-021-03569-z. ieee: S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” Journal of Ambient Intelligence and Humanized Computing, vol. 13. Springer Nature, pp. 2621–2635, 2022. 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. mla: Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” Journal of Ambient Intelligence and Humanized Computing, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:10.1007/s12652-021-03569-z. short: S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635. date_created: 2021-11-02T09:28:55Z date_published: 2022-05-01T00:00:00Z date_updated: 2023-08-02T13:31:48Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s12652-021-03569-z external_id: isi: - '000712198000001' file: - access_level: open_access checksum: 0a8961416a9bb2be5a1cebda65468bcf content_type: application/pdf creator: fkarimip date_created: 2021-11-12T19:38:05Z date_updated: 2022-12-20T23:30:08Z embargo: 2022-11-12 file_id: '10279' file_name: A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf file_size: 1634958 relation: main_file file_date_updated: 2022-12-20T23:30:08Z has_accepted_license: '1' intvolume: ' 13' isi: 1 keyword: - general computer science language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 2621–2635 project: - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize publication: Journal of Ambient Intelligence and Humanized Computing publication_identifier: eissn: - 1868-5145 issn: - 1868-5137 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A context-aware dimension reduction framework for trajectory and health signal analyses type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2022' ... --- _id: '10284' 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. acknowledged_ssus: - _id: ScienComp 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Filip full_name: Naiser, Filip last_name: Naiser - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Jiri full_name: Matas, Jiri last_name: Matas - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: 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. Ecology Letters. 2022;25(1):89-100. doi:10.1111/ele.13907 apa: Casillas Perez, B. E., 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. Wiley. https://doi.org/10.1111/ele.13907 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.” Ecology Letters. Wiley, 2022. https://doi.org/10.1111/ele.13907. 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,” Ecology Letters, vol. 25, no. 1. Wiley, pp. 89–100, 2022. 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. mla: Casillas Perez, Barbara E., et al. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Ecology Letters, vol. 25, no. 1, Wiley, 2022, pp. 89–100, doi:10.1111/ele.13907. short: B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100. date_created: 2021-11-14T23:01:25Z date_published: 2022-01-01T00:00:00Z date_updated: 2023-08-14T11:45:29Z day: '01' ddc: - '573' department: - _id: SyCr doi: 10.1111/ele.13907 ec_funded: 1 external_id: isi: - '000713396100001' pmid: - '34725912' file: - access_level: open_access checksum: 0bd4210400e9876609b7c538ab4f9a3c content_type: application/pdf creator: cchlebak date_created: 2022-02-03T13:37:11Z date_updated: 2022-02-03T13:37:11Z file_id: '10721' file_name: 2021_EcologyLetters_CasillasPerez.pdf file_size: 700087 relation: main_file success: 1 file_date_updated: 2022-02-03T13:37:11Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 89-100 pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publication: Ecology Letters publication_identifier: eissn: - 1461-0248 issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13061' relation: research_data status: public scopus_import: '1' status: public title: Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2022' ... --- _id: '10335' 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." 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.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Vojtech full_name: Kaluza, Vojtech id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E last_name: Kaluza orcid: 0000-0002-2512-8698 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 citation: ama: Kaluza V, Tancer M. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 2022;42:1317-1345. doi:10.1007/s00493-021-4443-7 apa: Kaluza, V., & Tancer, M. (2022). Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-021-4443-7 chicago: Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” Combinatorica. Springer Nature, 2022. https://doi.org/10.1007/s00493-021-4443-7. ieee: V. Kaluza and M. Tancer, “Even maps, the Colin de Verdière number and representations of graphs,” Combinatorica, vol. 42. Springer Nature, pp. 1317–1345, 2022. ista: Kaluza V, Tancer M. 2022. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 42, 1317–1345. mla: Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” Combinatorica, vol. 42, Springer Nature, 2022, pp. 1317–45, doi:10.1007/s00493-021-4443-7. short: V. Kaluza, M. Tancer, Combinatorica 42 (2022) 1317–1345. date_created: 2021-11-25T13:49:16Z date_published: 2022-12-01T00:00:00Z date_updated: 2023-08-02T06:43:27Z day: '01' ddc: - '514' - '516' department: - _id: UlWa doi: 10.1007/s00493-021-4443-7 external_id: arxiv: - '1907.05055' isi: - '000798210100003' intvolume: ' 42' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1907.05055' month: '12' oa: 1 oa_version: Preprint page: 1317-1345 publication: Combinatorica publication_identifier: issn: - 0209-9683 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Even maps, the Colin de Verdière number and representations of graphs type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 42 year: '2022' ... --- _id: '10364' abstract: - lang: eng 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.' 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." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Arman full_name: Fazeli, Arman last_name: Fazeli - first_name: Alexander full_name: Vardy, Alexander last_name: Vardy - first_name: John full_name: Cioffi, John last_name: Cioffi - first_name: Andrea full_name: Goldsmith, Andrea last_name: Goldsmith 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. IEEE Transactions on Wireless Communications. 2022;21(6):3909-3920. doi:10.1109/TWC.2021.3125626 apa: Hashemi, S. A., 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. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TWC.2021.3125626 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.” IEEE Transactions on Wireless Communications. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/TWC.2021.3125626. 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,” IEEE Transactions on Wireless Communications, vol. 21, no. 6. Institute of Electrical and Electronics Engineers, pp. 3909–3920, 2022. 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. mla: Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” IEEE Transactions on Wireless Communications, vol. 21, no. 6, Institute of Electrical and Electronics Engineers, 2022, pp. 3909–20, doi:10.1109/TWC.2021.3125626. short: S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920. date_created: 2021-11-28T23:01:29Z date_published: 2022-06-01T00:00:00Z date_updated: 2024-09-10T13:03:18Z day: '01' department: - _id: MaMo doi: 10.1109/TWC.2021.3125626 external_id: arxiv: - '2012.13378' isi: - '000809406400028' intvolume: ' 21' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.13378 month: '06' oa: 1 oa_version: Preprint page: 3909-3920 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: IEEE Transactions on Wireless Communications publication_identifier: eissn: - 1558-2248 issn: - 1536-1276 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' related_material: record: - id: '10053' relation: earlier_version status: public scopus_import: '1' status: public title: Parallelism versus latency in simplified successive-cancellation decoding of polar codes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2022' ... --- _id: '10411' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Li L, Gallei MC, Friml J. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 2022;27(5):440-449. doi:10.1016/j.tplants.2021.11.006' apa: 'Li, L., Gallei, M. C., & Friml, J. (2022). Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2021.11.006' chicago: 'Li, Lanxin, Michelle C Gallei, and Jiří Friml. “Bending to Auxin: Fast Acid Growth for Tropisms.” Trends in Plant Science. Cell Press, 2022. https://doi.org/10.1016/j.tplants.2021.11.006.' ieee: 'L. Li, M. C. Gallei, and J. Friml, “Bending to auxin: Fast acid growth for tropisms,” Trends in Plant Science, vol. 27, no. 5. Cell Press, pp. 440–449, 2022.' ista: 'Li L, Gallei MC, Friml J. 2022. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 27(5), 440–449.' mla: 'Li, Lanxin, et al. “Bending to Auxin: Fast Acid Growth for Tropisms.” Trends in Plant Science, vol. 27, no. 5, Cell Press, 2022, pp. 440–49, doi:10.1016/j.tplants.2021.11.006.' short: L. Li, M.C. Gallei, J. Friml, Trends in Plant Science 27 (2022) 440–449. date_created: 2021-12-05T23:01:43Z date_published: 2022-05-01T00:00:00Z date_updated: 2024-10-29T10:12:33Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.tplants.2021.11.006 external_id: isi: - '000793707900005' pmid: - '34848141' file: - access_level: open_access checksum: 3d94980ee1ff6bec100dd813f6a921a6 content_type: application/pdf creator: amally date_created: 2023-11-02T17:00:03Z date_updated: 2023-11-02T17:00:03Z file_id: '14480' file_name: Li Plants 2021_accepted.pdf file_size: 805779 relation: main_file success: 1 file_date_updated: 2023-11-02T17:00:03Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 440-449 pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Trends in Plant Science publication_identifier: issn: - 1360-1385 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '11626' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Bending to auxin: Fast acid growth for tropisms' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2022' ... --- _id: '10413' abstract: - lang: eng 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. acknowledgement: Dedicated to the memory of Hans-Peter Künzi. article_number: '107916' article_processing_charge: No article_type: original author: - first_name: Dikran full_name: Dikranjan, Dikran last_name: Dikranjan - first_name: Anna full_name: Giordano Bruno, Anna last_name: Giordano Bruno - first_name: Hans Peter full_name: Künzi, Hans Peter last_name: Künzi - first_name: Nicolò full_name: Zava, Nicolò id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad last_name: Zava orcid: 0000-0001-8686-1888 - first_name: Daniele full_name: Toller, Daniele last_name: Toller citation: ama: Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. Generalized quasi-metric semilattices. Topology and its Applications. 2022;309. doi:10.1016/j.topol.2021.107916 apa: Dikranjan, D., Giordano Bruno, A., Künzi, H. P., Zava, N., & Toller, D. (2022). Generalized quasi-metric semilattices. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2021.107916 chicago: Dikranjan, Dikran, Anna Giordano Bruno, Hans Peter Künzi, Nicolò Zava, and Daniele Toller. “Generalized Quasi-Metric Semilattices.” Topology and Its Applications. Elsevier, 2022. https://doi.org/10.1016/j.topol.2021.107916. ieee: D. Dikranjan, A. Giordano Bruno, H. P. Künzi, N. Zava, and D. Toller, “Generalized quasi-metric semilattices,” Topology and its Applications, vol. 309. Elsevier, 2022. ista: Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized quasi-metric semilattices. Topology and its Applications. 309, 107916. mla: Dikranjan, Dikran, et al. “Generalized Quasi-Metric Semilattices.” Topology and Its Applications, vol. 309, 107916, Elsevier, 2022, doi:10.1016/j.topol.2021.107916. short: D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology and Its Applications 309 (2022). date_created: 2021-12-05T23:01:44Z date_published: 2022-03-15T00:00:00Z date_updated: 2023-08-02T13:33:24Z day: '15' department: - _id: HeEd doi: 10.1016/j.topol.2021.107916 external_id: isi: - '000791838800012' intvolume: ' 309' isi: 1 language: - iso: eng month: '03' oa_version: None publication: Topology and its Applications publication_identifier: issn: - 0166-8641 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Generalized quasi-metric semilattices type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 309 year: '2022' ... --- _id: '10530' abstract: - lang: eng 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" 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. article_processing_charge: No article_type: original author: - first_name: Themistoklis full_name: Zisis, Themistoklis last_name: Zisis - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Tom full_name: Brandstätter, Tom last_name: Brandstätter - first_name: Wei Xiong full_name: Siow, Wei Xiong last_name: Siow - first_name: Joseph full_name: d’Alessandro, Joseph last_name: d’Alessandro - first_name: Angelika M. full_name: Vollmar, Angelika M. last_name: Vollmar - first_name: Chase P. full_name: Broedersz, Chase P. last_name: Broedersz - first_name: Stefan full_name: Zahler, Stefan last_name: Zahler citation: ama: Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006 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. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006 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.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006. ieee: T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” Biophysical Journal, vol. 121, no. 1. Elsevier, pp. P44-60, 2022. 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. mla: Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:10.1016/j.bpj.2021.12.006. 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. date_created: 2021-12-10T09:48:19Z date_published: 2022-01-04T00:00:00Z date_updated: 2023-08-02T13:34:25Z day: '04' ddc: - '570' department: - _id: EdHa - _id: GaTk doi: 10.1016/j.bpj.2021.12.006 external_id: isi: - '000740815400007' file: - access_level: open_access checksum: 1aa7c3478e0c8256b973b632efd1f6b4 content_type: application/pdf creator: dernst date_created: 2022-07-29T10:17:10Z date_updated: 2022-07-29T10:17:10Z file_id: '11697' file_name: 2022_BiophysicalJour_Zisis.pdf file_size: 4475504 relation: main_file success: 1 file_date_updated: 2022-07-29T10:17:10Z has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '1' keyword: - Biophysics language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: P44-60 project: - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration 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) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 121 year: '2022' ... --- _id: '10547' abstract: - lang: eng 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." 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). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Katharina full_name: Hopf, Katharina last_name: Hopf - first_name: Michael full_name: Kniely, Michael id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87 last_name: Kniely orcid: 0000-0001-5645-4333 - first_name: Alexander full_name: Mielke, Alexander last_name: Mielke citation: ama: Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 2022;54(1):220-267. doi:10.1137/20M1387237 apa: Fischer, J. L., Hopf, K., Kniely, M., & Mielke, A. (2022). Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1387237 chicago: Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2022. https://doi.org/10.1137/20M1387237. ieee: J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis of energy-reaction-diffusion systems,” SIAM Journal on Mathematical Analysis, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022. 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. mla: Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” SIAM Journal on Mathematical Analysis, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:10.1137/20M1387237. short: J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical Analysis 54 (2022) 220–267. date_created: 2021-12-16T12:08:56Z date_published: 2022-01-04T00:00:00Z date_updated: 2023-08-02T13:37:03Z day: '04' department: - _id: JuFi doi: 10.1137/20M1387237 external_id: arxiv: - '2012.03792 ' isi: - '000762768000006' intvolume: ' 54' isi: 1 issue: '1' keyword: - Energy-Reaction-Diffusion Systems - Cross Diffusion - Global-In-Time Existence of Weak/Renormalised Solutions - Entropy Method - Onsager System - Soret/Dufour Effect language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.03792 month: '01' oa: 1 oa_version: Preprint page: 220-267 publication: SIAM Journal on Mathematical Analysis publication_identifier: issn: - 0036-1410 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Global existence analysis of energy-reaction-diffusion systems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 54 year: '2022' ...