--- _id: '14355' abstract: - lang: eng text: 'Purpose: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. Methods: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. Results: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. Conclusion: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.' article_processing_charge: No article_type: original author: - first_name: Elisa full_name: Cali, Elisa last_name: Cali - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Clarissa full_name: Rocca, Clarissa last_name: Rocca - first_name: Yavuz full_name: Sahin, Yavuz last_name: Sahin - first_name: Aisha full_name: Al Shamsi, Aisha last_name: Al Shamsi - first_name: Salima full_name: El Chehadeh, Salima last_name: El Chehadeh - first_name: Myriam full_name: Chaabouni, Myriam last_name: Chaabouni - first_name: Kshitij full_name: Mankad, Kshitij last_name: Mankad - first_name: Evangelia full_name: Galanaki, Evangelia last_name: Galanaki - first_name: Stephanie full_name: Efthymiou, Stephanie last_name: Efthymiou - first_name: Sniya full_name: Sudhakar, Sniya last_name: Sudhakar - first_name: Alkyoni full_name: Athanasiou-Fragkouli, Alkyoni last_name: Athanasiou-Fragkouli - first_name: Tamer full_name: Celik, Tamer last_name: Celik - first_name: Nejat full_name: Narli, Nejat last_name: Narli - first_name: Sebastiano full_name: Bianca, Sebastiano last_name: Bianca - first_name: David full_name: Murphy, David last_name: Murphy - first_name: Francisco Martins De Carvalho full_name: Moreira, Francisco Martins De Carvalho last_name: Moreira - first_name: Andrea full_name: Accogli, Andrea last_name: Accogli - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Kamel full_name: Monastiri, Kamel last_name: Monastiri - first_name: Masoud full_name: Edizadeh, Masoud last_name: Edizadeh - first_name: Rosaria full_name: Nardello, Rosaria last_name: Nardello - first_name: Marzia full_name: Ognibene, Marzia last_name: Ognibene - first_name: Patrizia full_name: De Marco, Patrizia last_name: De Marco - first_name: Martino full_name: Ruggieri, Martino last_name: Ruggieri - first_name: Federico full_name: Zara, Federico last_name: Zara - first_name: Pasquale full_name: Striano, Pasquale last_name: Striano - first_name: Yavuz full_name: Sahin, Yavuz last_name: Sahin - first_name: Lihadh full_name: Al-Gazali, Lihadh last_name: Al-Gazali - first_name: Marie Therese Abi full_name: Warde, Marie Therese Abi last_name: Warde - first_name: Benedicte full_name: Gerard, Benedicte last_name: Gerard - first_name: Giovanni full_name: Zifarelli, Giovanni last_name: Zifarelli - first_name: Christian full_name: Beetz, Christian last_name: Beetz - first_name: Sara full_name: Fortuna, Sara last_name: Fortuna - first_name: Miguel full_name: Soler, Miguel last_name: Soler - first_name: Enza Maria full_name: Valente, Enza Maria last_name: Valente - first_name: Gaurav full_name: Varshney, Gaurav last_name: Varshney - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian - first_name: Vincenzo full_name: Salpietro, Vincenzo last_name: Salpietro - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: SYNaPS Study full_name: Grp, SYNaPS Study last_name: Grp citation: ama: Cali E, Lin S-J, Rocca C, et al. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 2022;24(10):2194-2203. doi:10.1016/j.gim.2022.07.013 apa: Cali, E., Lin, S.-J., Rocca, C., Sahin, Y., Al Shamsi, A., El Chehadeh, S., … Grp, Syn. S. (2022). A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. Elsevier. https://doi.org/10.1016/j.gim.2022.07.013 chicago: Cali, Elisa, Sheng-Jia Lin, Clarissa Rocca, Yavuz Sahin, Aisha Al Shamsi, Salima El Chehadeh, Myriam Chaabouni, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” Genetics in Medicine. Elsevier, 2022. https://doi.org/10.1016/j.gim.2022.07.013. ieee: E. Cali et al., “A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease,” Genetics in Medicine, vol. 24, no. 10. Elsevier, pp. 2194–2203, 2022. ista: Cali E, Lin S-J, Rocca C, Sahin Y, Al Shamsi A, El Chehadeh S, Chaabouni M, Mankad K, Galanaki E, Efthymiou S, Sudhakar S, Athanasiou-Fragkouli A, Celik T, Narli N, Bianca S, Murphy D, Moreira FMDC, Accogli A, Petree C, Huang K, Monastiri K, Edizadeh M, Nardello R, Ognibene M, De Marco P, Ruggieri M, Zara F, Striano P, Sahin Y, Al-Gazali L, Warde MTA, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H, Grp SynS. 2022. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 24(10), 2194–2203. mla: Cali, Elisa, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” Genetics in Medicine, vol. 24, no. 10, Elsevier, 2022, pp. 2194–203, doi:10.1016/j.gim.2022.07.013. short: E. Cali, S.-J. Lin, C. Rocca, Y. Sahin, A. Al Shamsi, S. El Chehadeh, M. Chaabouni, K. Mankad, E. Galanaki, S. Efthymiou, S. Sudhakar, A. Athanasiou-Fragkouli, T. Celik, N. Narli, S. Bianca, D. Murphy, F.M.D.C. Moreira, A. Accogli, C. Petree, K. Huang, K. Monastiri, M. Edizadeh, R. Nardello, M. Ognibene, P. De Marco, M. Ruggieri, F. Zara, P. Striano, Y. Sahin, L. Al-Gazali, M.T.A. Warde, B. Gerard, G. Zifarelli, C. Beetz, S. Fortuna, M. Soler, E.M. Valente, G. Varshney, R. Maroofian, V. Salpietro, H. Houlden, Syn.S. Grp, Genetics in Medicine 24 (2022) 2194–2203. date_created: 2023-09-20T20:57:18Z date_published: 2022-10-01T00:00:00Z date_updated: 2023-09-25T08:57:07Z day: '01' ddc: - '570' department: - _id: GradSch doi: 10.1016/j.gim.2022.07.013 extern: '1' file: - access_level: open_access checksum: 8117175a89129eb5022d81ffe7625f9f content_type: application/pdf creator: dernst date_created: 2023-09-25T08:56:06Z date_updated: 2023-09-25T08:56:06Z file_id: '14371' file_name: 2022_GeneticsMedicine_Calin.pdf file_size: 1434037 relation: main_file success: 1 file_date_updated: 2023-09-25T08:56:06Z has_accepted_license: '1' intvolume: ' 24' issue: '10' keyword: - Human mediator complex - MED11 - MEDopathies language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 2194-2203 publication: Genetics in Medicine publication_identifier: issn: - 1098-3600 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease 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: 24 year: '2022' ... --- _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. corr_author: '1' date_created: 2023-10-01T22:01:14Z date_published: 2022-01-01T00:00:00Z date_updated: 2025-09-10T09:55:10Z day: '01' department: - _id: UlWa doi: 10.24033/ast.1188 external_id: isi: - '000958364400007' intvolume: ' 438' isi: 1 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 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. corr_author: '1' date_created: 2023-10-17T11:14:43Z date_published: 2022-12-21T00:00:00Z date_updated: 2025-09-10T09:55:51Z day: '21' department: - _id: MaIb doi: 10.1038/d41586-022-04447-0 external_id: isi: - '000934065100010' pmid: - '36543947' intvolume: ' 612' isi: 1 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' scopus_import: '1' status: public title: Molecular engineering enables bright blue LEDs type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 612 year: '2022' ... --- OA_place: repository OA_type: green _id: '17868' abstract: - lang: eng text: Reversed conductance decay describes increasing conductance of a molecular chain series with increasing chain length. Realizing reversed conductance decay is an important step toward making long and highly conducting molecular wires. Recent work has shown that one-dimensional topological insulators (1D TIs) can exhibit reversed conductance decay due to their nontrivial edge states. The Su–Schrieffer–Heeger (SSH) model for 1D TIs relates to the electronic structure of these isolated molecules but not their electron transport properties as single-molecule junctions. Herein, we use a tight-binding approach to demonstrate that polyacetylene and other diradicaloid 1D TIs show a reversed conductance decay at the short chain limit. We explain these conductance trends by analyzing the impact of the edge states in these 1D systems on the single-molecule junction transmission. Additionally, we discuss how the self-energy from the electrode-molecule coupling and the on-site energy of the edge sites can be tuned to create longer wires with reversed conductance decays. article_processing_charge: No article_type: original author: - first_name: Liang full_name: Li, Liang last_name: Li - first_name: Suman full_name: Gunasekaran, Suman last_name: Gunasekaran - first_name: Yujing full_name: Wei, Yujing last_name: Wei - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Li L, Gunasekaran S, Wei Y, Nuckolls C, Venkataraman L. Reversed conductance decay of 1D topological insulators by tight-binding analysis. The Journal of Physical Chemistry Letters. 2022;13(41):9703-9710. doi:10.1021/acs.jpclett.2c02812 apa: Li, L., Gunasekaran, S., Wei, Y., Nuckolls, C., & Venkataraman, L. (2022). Reversed conductance decay of 1D topological insulators by tight-binding analysis. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.2c02812 chicago: Li, Liang, Suman Gunasekaran, Yujing Wei, Colin Nuckolls, and Latha Venkataraman. “Reversed Conductance Decay of 1D Topological Insulators by Tight-Binding Analysis.” The Journal of Physical Chemistry Letters. American Chemical Society, 2022. https://doi.org/10.1021/acs.jpclett.2c02812. ieee: L. Li, S. Gunasekaran, Y. Wei, C. Nuckolls, and L. Venkataraman, “Reversed conductance decay of 1D topological insulators by tight-binding analysis,” The Journal of Physical Chemistry Letters, vol. 13, no. 41. American Chemical Society, pp. 9703–9710, 2022. ista: Li L, Gunasekaran S, Wei Y, Nuckolls C, Venkataraman L. 2022. Reversed conductance decay of 1D topological insulators by tight-binding analysis. The Journal of Physical Chemistry Letters. 13(41), 9703–9710. mla: Li, Liang, et al. “Reversed Conductance Decay of 1D Topological Insulators by Tight-Binding Analysis.” The Journal of Physical Chemistry Letters, vol. 13, no. 41, American Chemical Society, 2022, pp. 9703–10, doi:10.1021/acs.jpclett.2c02812. short: L. Li, S. Gunasekaran, Y. Wei, C. Nuckolls, L. Venkataraman, The Journal of Physical Chemistry Letters 13 (2022) 9703–9710. date_created: 2024-09-06T13:02:46Z date_published: 2022-10-11T00:00:00Z date_updated: 2024-12-10T09:21:49Z day: '11' doi: 10.1021/acs.jpclett.2c02812 extern: '1' external_id: pmid: - '36219846' intvolume: ' 13' issue: '41' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv-2022-b1fh9-v3 month: '10' oa: 1 oa_version: Preprint page: 9703-9710 pmid: 1 publication: The Journal of Physical Chemistry Letters publication_identifier: issn: - 1948-7185 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Reversed conductance decay of 1D topological insulators by tight-binding analysis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2022' ... --- OA_place: repository OA_type: green _id: '17869' abstract: - lang: eng text: The formation of carbon–carbon bonds with transition metal reagents serves as a cornerstone of organic synthesis. Here, we show that the reactivity of an otherwise kinetically inert transition metal complex can be induced by an external electric field to affect a coupling reaction. These results highlight the importance of electric field effects in reaction chemistry and offers a new strategy to modulate organometallic reactivity. article_processing_charge: No article_type: letter_note author: - first_name: Nicholas M. full_name: Orchanian, Nicholas M. last_name: Orchanian - first_name: Sophia full_name: Guizzo, Sophia last_name: Guizzo - first_name: Michael L. full_name: Steigerwald, Michael L. last_name: Steigerwald - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Orchanian NM, Guizzo S, Steigerwald ML, Nuckolls C, Venkataraman L. Electric-field-induced coupling of aryl iodides with a nickel(0) complex. Chemical Communications. 2022;58(90):12556-12559. doi:10.1039/d2cc03671a apa: Orchanian, N. M., Guizzo, S., Steigerwald, M. L., Nuckolls, C., & Venkataraman, L. (2022). Electric-field-induced coupling of aryl iodides with a nickel(0) complex. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/d2cc03671a chicago: Orchanian, Nicholas M., Sophia Guizzo, Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. “Electric-Field-Induced Coupling of Aryl Iodides with a Nickel(0) Complex.” Chemical Communications. Royal Society of Chemistry, 2022. https://doi.org/10.1039/d2cc03671a. ieee: N. M. Orchanian, S. Guizzo, M. L. Steigerwald, C. Nuckolls, and L. Venkataraman, “Electric-field-induced coupling of aryl iodides with a nickel(0) complex,” Chemical Communications, vol. 58, no. 90. Royal Society of Chemistry, pp. 12556–12559, 2022. ista: Orchanian NM, Guizzo S, Steigerwald ML, Nuckolls C, Venkataraman L. 2022. Electric-field-induced coupling of aryl iodides with a nickel(0) complex. Chemical Communications. 58(90), 12556–12559. mla: Orchanian, Nicholas M., et al. “Electric-Field-Induced Coupling of Aryl Iodides with a Nickel(0) Complex.” Chemical Communications, vol. 58, no. 90, Royal Society of Chemistry, 2022, pp. 12556–59, doi:10.1039/d2cc03671a. short: N.M. Orchanian, S. Guizzo, M.L. Steigerwald, C. Nuckolls, L. Venkataraman, Chemical Communications 58 (2022) 12556–12559. date_created: 2024-09-06T13:03:38Z date_published: 2022-10-10T00:00:00Z date_updated: 2024-12-10T09:27:04Z day: '10' doi: 10.1039/d2cc03671a extern: '1' external_id: pmid: - '36245392' intvolume: ' 58' issue: '90' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv-2022-lfnw1 month: '10' oa: 1 oa_version: Preprint page: 12556-12559 pmid: 1 publication: Chemical Communications publication_identifier: eissn: - 1364-548X issn: - 1359-7345 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1039/d2cc03671a scopus_import: '1' status: public title: Electric-field-induced coupling of aryl iodides with a nickel(0) complex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2022' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17870' abstract: - lang: eng text: The electric fields created at solid–liquid interfaces are important in heterogeneous catalysis. Here we describe the Ullmann coupling of aryl iodides on rough gold surfaces, which we monitor in situ using the scanning tunneling microscope-based break junction (STM-BJ) and ex situ using mass spectrometry and fluorescence spectroscopy. We find that this Ullmann coupling reaction occurs only on rough gold surfaces in polar solvents, the latter of which implicates interfacial electric fields. These experimental observations are supported by density functional theory calculations that elucidate the roles of surface roughness and local electric fields on the reaction. More broadly, this touchstone study offers a facile method to access and probe in real time an increasingly prominent yet incompletely understood mode of catalysis. article_processing_charge: Yes article_type: original author: - first_name: Ilana B. full_name: Stone, Ilana B. last_name: Stone - first_name: Rachel L. full_name: Starr, Rachel L. last_name: Starr - first_name: Norah full_name: Hoffmann, Norah last_name: Hoffmann - first_name: Xiao full_name: Wang, Xiao last_name: Wang - first_name: Austin M. full_name: Evans, Austin M. last_name: Evans - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Tristan H. full_name: Lambert, Tristan H. last_name: Lambert - first_name: Michael L. full_name: Steigerwald, Michael L. last_name: Steigerwald - first_name: Timothy C. full_name: Berkelbach, Timothy C. last_name: Berkelbach - first_name: Xavier full_name: Roy, Xavier last_name: Roy - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Stone IB, Starr RL, Hoffmann N, et al. Interfacial electric fields catalyze Ullmann coupling reactions on gold surfaces. Chemical Science. 2022;13(36):10798-10805. doi:10.1039/d2sc03780g apa: Stone, I. B., Starr, R. L., Hoffmann, N., Wang, X., Evans, A. M., Nuckolls, C., … Venkataraman, L. (2022). Interfacial electric fields catalyze Ullmann coupling reactions on gold surfaces. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d2sc03780g chicago: Stone, Ilana B., Rachel L. Starr, Norah Hoffmann, Xiao Wang, Austin M. Evans, Colin Nuckolls, Tristan H. Lambert, et al. “Interfacial Electric Fields Catalyze Ullmann Coupling Reactions on Gold Surfaces.” Chemical Science. Royal Society of Chemistry, 2022. https://doi.org/10.1039/d2sc03780g. ieee: I. B. Stone et al., “Interfacial electric fields catalyze Ullmann coupling reactions on gold surfaces,” Chemical Science, vol. 13, no. 36. Royal Society of Chemistry, pp. 10798–10805, 2022. ista: Stone IB, Starr RL, Hoffmann N, Wang X, Evans AM, Nuckolls C, Lambert TH, Steigerwald ML, Berkelbach TC, Roy X, Venkataraman L. 2022. Interfacial electric fields catalyze Ullmann coupling reactions on gold surfaces. Chemical Science. 13(36), 10798–10805. mla: Stone, Ilana B., et al. “Interfacial Electric Fields Catalyze Ullmann Coupling Reactions on Gold Surfaces.” Chemical Science, vol. 13, no. 36, Royal Society of Chemistry, 2022, pp. 10798–805, doi:10.1039/d2sc03780g. short: I.B. Stone, R.L. Starr, N. Hoffmann, X. Wang, A.M. Evans, C. Nuckolls, T.H. Lambert, M.L. Steigerwald, T.C. Berkelbach, X. Roy, L. Venkataraman, Chemical Science 13 (2022) 10798–10805. date_created: 2024-09-06T13:04:27Z date_published: 2022-09-01T00:00:00Z date_updated: 2024-12-10T09:29:53Z day: '01' doi: 10.1039/d2sc03780g extern: '1' intvolume: ' 13' issue: '36' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1039/D2SC03780G month: '09' oa: 1 oa_version: Published Version page: 10798-10805 publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Interfacial electric fields catalyze Ullmann coupling reactions on gold surfaces tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2022' ... --- OA_type: closed access _id: '17871' abstract: - lang: eng text: Single-molecule topological insulators are promising candidates as conducting wires over nanometre length scales. A key advantage is their ability to exhibit quasi-metallic transport, in contrast to conjugated molecular wires which typically exhibit a low conductance that decays as the wire length increases. Here, we study a family of oligophenylene-bridged bis(triarylamines) with tunable and stable mono- or di-radicaloid character. These wires can undergo one- and two-electron chemical oxidations to the corresponding mono-cation and di-cation, respectively. We show that the oxidized wires exhibit reversed conductance decay with increasing length, consistent with the expectation for Su–Schrieffer–Heeger-type one-dimensional topological insulators. The 2.6-nm-long di-cation reported here displays a conductance greater than 0.1G0, where G0 is the conductance quantum, a factor of 5,400 greater than the neutral form. The observed conductance–length relationship is similar between the mono-cation and di-cation series. Density functional theory calculations elucidate how the frontier orbitals and delocalization of radicals facilitate the observed non-classical quasi-metallic behaviour. article_processing_charge: No article_type: original author: - first_name: Liang full_name: Li, Liang last_name: Li - first_name: Jonathan Z. full_name: Low, Jonathan Z. last_name: Low - first_name: Jan full_name: Wilhelm, Jan last_name: Wilhelm - first_name: Guanming full_name: Liao, Guanming last_name: Liao - first_name: Suman full_name: Gunasekaran, Suman last_name: Gunasekaran - first_name: Claudia R. full_name: Prindle, Claudia R. last_name: Prindle - first_name: Rachel L. full_name: Starr, Rachel L. last_name: Starr - first_name: Dorothea full_name: Golze, Dorothea last_name: Golze - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Michael L. full_name: Steigerwald, Michael L. last_name: Steigerwald - first_name: Ferdinand full_name: Evers, Ferdinand last_name: Evers - first_name: Luis M. full_name: Campos, Luis M. last_name: Campos - first_name: Xiaodong full_name: Yin, Xiaodong last_name: Yin - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Li L, Low JZ, Wilhelm J, et al. Highly conducting single-molecule topological insulators based on mono- and di-radical cations. Nature Chemistry. 2022;14(9):1061-1067. doi:10.1038/s41557-022-00978-1 apa: Li, L., Low, J. Z., Wilhelm, J., Liao, G., Gunasekaran, S., Prindle, C. R., … Venkataraman, L. (2022). Highly conducting single-molecule topological insulators based on mono- and di-radical cations. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-022-00978-1 chicago: Li, Liang, Jonathan Z. Low, Jan Wilhelm, Guanming Liao, Suman Gunasekaran, Claudia R. Prindle, Rachel L. Starr, et al. “Highly Conducting Single-Molecule Topological Insulators Based on Mono- and Di-Radical Cations.” Nature Chemistry. Springer Nature, 2022. https://doi.org/10.1038/s41557-022-00978-1. ieee: L. Li et al., “Highly conducting single-molecule topological insulators based on mono- and di-radical cations,” Nature Chemistry, vol. 14, no. 9. Springer Nature, pp. 1061–1067, 2022. ista: Li L, Low JZ, Wilhelm J, Liao G, Gunasekaran S, Prindle CR, Starr RL, Golze D, Nuckolls C, Steigerwald ML, Evers F, Campos LM, Yin X, Venkataraman L. 2022. Highly conducting single-molecule topological insulators based on mono- and di-radical cations. Nature Chemistry. 14(9), 1061–1067. mla: Li, Liang, et al. “Highly Conducting Single-Molecule Topological Insulators Based on Mono- and Di-Radical Cations.” Nature Chemistry, vol. 14, no. 9, Springer Nature, 2022, pp. 1061–67, doi:10.1038/s41557-022-00978-1. short: L. Li, J.Z. Low, J. Wilhelm, G. Liao, S. Gunasekaran, C.R. Prindle, R.L. Starr, D. Golze, C. Nuckolls, M.L. Steigerwald, F. Evers, L.M. Campos, X. Yin, L. Venkataraman, Nature Chemistry 14 (2022) 1061–1067. date_created: 2024-09-06T13:05:31Z date_published: 2022-07-07T00:00:00Z date_updated: 2024-12-10T09:37:45Z day: '07' doi: 10.1038/s41557-022-00978-1 extern: '1' external_id: pmid: - '35798950' intvolume: ' 14' issue: '9' language: - iso: eng month: '07' oa_version: None page: 1061-1067 pmid: 1 publication: Nature Chemistry publication_identifier: eissn: - 1755-4349 issn: - 1755-4330 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Highly conducting single-molecule topological insulators based on mono- and di-radical cations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2022' ... --- _id: '17872' abstract: - lang: eng text: Coherent tunneling electron transport through molecular wires has been theoretically established as a temperature-independent process. Although several experimental studies have shown counter examples, robust models to describe this temperature dependence have not been thoroughly developed. Here, we demonstrate that dynamic molecular structures lead to temperature-dependent conductance within coherent tunneling regime. Using a custom-built variable-temperature scanning tunneling microscopy break-junction instrument, we find that oligo[n]phenylenes exhibit clear temperature-dependent conductance. Our calculations reveal that thermally activated dihedral rotations allow these molecular wires to have a higher probability of being in a planar conformation. As the tunneling occurs primarily through π-orbitals, enhanced coplanarization substantially increases the time-averaged tunneling probability. These calculations are consistent with the observation that more rotational pivot points in longer molecular wires leads to larger temperature-dependence on conductance. These findings reveal that molecular conductance within coherent and off-resonant electron transport regimes can be controlled by manipulating dynamic molecular structure. article_processing_charge: No article_type: letter_note author: - first_name: Woojung full_name: Lee, Woojung last_name: Lee - first_name: Shayan full_name: Louie, Shayan last_name: Louie - first_name: Austin M. full_name: Evans, Austin M. last_name: Evans - first_name: Nicholas M. full_name: Orchanian, Nicholas M. last_name: Orchanian - first_name: Ilana B. full_name: Stone, Ilana B. last_name: Stone - first_name: Boyuan full_name: Zhang, Boyuan last_name: Zhang - first_name: Yujing full_name: Wei, Yujing last_name: Wei - first_name: Xavier full_name: Roy, Xavier last_name: Roy - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Lee W, Louie S, Evans AM, et al. Increased molecular conductance in Oligo[n]phenylene wires by thermally enhanced dihedral planarization. Nano Letters. 2022;22(12):4919-4924. doi:10.1021/acs.nanolett.2c01549 apa: Lee, W., Louie, S., Evans, A. M., Orchanian, N. M., Stone, I. B., Zhang, B., … Venkataraman, L. (2022). Increased molecular conductance in Oligo[n]phenylene wires by thermally enhanced dihedral planarization. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.2c01549 chicago: Lee, Woojung, Shayan Louie, Austin M. Evans, Nicholas M. Orchanian, Ilana B. Stone, Boyuan Zhang, Yujing Wei, Xavier Roy, Colin Nuckolls, and Latha Venkataraman. “Increased Molecular Conductance in Oligo[n]Phenylene Wires by Thermally Enhanced Dihedral Planarization.” Nano Letters. American Chemical Society, 2022. https://doi.org/10.1021/acs.nanolett.2c01549. ieee: W. Lee et al., “Increased molecular conductance in Oligo[n]phenylene wires by thermally enhanced dihedral planarization,” Nano Letters, vol. 22, no. 12. American Chemical Society, pp. 4919–4924, 2022. ista: Lee W, Louie S, Evans AM, Orchanian NM, Stone IB, Zhang B, Wei Y, Roy X, Nuckolls C, Venkataraman L. 2022. Increased molecular conductance in Oligo[n]phenylene wires by thermally enhanced dihedral planarization. Nano Letters. 22(12), 4919–4924. mla: Lee, Woojung, et al. “Increased Molecular Conductance in Oligo[n]Phenylene Wires by Thermally Enhanced Dihedral Planarization.” Nano Letters, vol. 22, no. 12, American Chemical Society, 2022, pp. 4919–24, doi:10.1021/acs.nanolett.2c01549. short: W. Lee, S. Louie, A.M. Evans, N.M. Orchanian, I.B. Stone, B. Zhang, Y. Wei, X. Roy, C. Nuckolls, L. Venkataraman, Nano Letters 22 (2022) 4919–4924. date_created: 2024-09-06T13:06:35Z date_published: 2022-05-31T00:00:00Z date_updated: 2024-12-10T09:40:39Z day: '31' doi: 10.1021/acs.nanolett.2c01549 extern: '1' external_id: pmid: - '35640062' intvolume: ' 22' issue: '12' language: - iso: eng month: '05' oa_version: None page: 4919-4924 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Increased molecular conductance in Oligo[n]phenylene wires by thermally enhanced dihedral planarization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2022' ... --- OA_place: repository OA_type: green _id: '17873' abstract: - lang: eng text: AbstractA critical overview of the theory of the chirality‐induced spin selectivity (CISS) effect, that is, phenomena in which the chirality of molecular species imparts significant spin selectivity to various electron processes, is provided. Based on discussions in a recently held workshop, and further work published since, the status of CISS effects—in electron transmission, electron transport, and chemical reactions—is reviewed. For each, a detailed discussion of the state‐of‐the‐art in theoretical understanding is provided and remaining challenges and research opportunities are identified. article_number: '2106629' article_processing_charge: No article_type: review arxiv: 1 author: - first_name: Ferdinand full_name: Evers, Ferdinand last_name: Evers - first_name: Amnon full_name: Aharony, Amnon last_name: Aharony - first_name: Nir full_name: Bar‐Gill, Nir last_name: Bar‐Gill - first_name: Ora full_name: Entin‐Wohlman, Ora last_name: Entin‐Wohlman - first_name: Per full_name: Hedegård, Per last_name: Hedegård - first_name: Oded full_name: Hod, Oded last_name: Hod - first_name: Pavel full_name: Jelinek, Pavel last_name: Jelinek - first_name: Grzegorz full_name: Kamieniarz, Grzegorz last_name: Kamieniarz - first_name: Mikhail full_name: Lemeshko, Mikhail last_name: Lemeshko - first_name: Karen full_name: Michaeli, Karen last_name: Michaeli - first_name: Vladimiro full_name: Mujica, Vladimiro last_name: Mujica - first_name: Ron full_name: Naaman, Ron last_name: Naaman - first_name: Yossi full_name: Paltiel, Yossi last_name: Paltiel - first_name: Sivan full_name: Refaely‐Abramson, Sivan last_name: Refaely‐Abramson - first_name: Oren full_name: Tal, Oren last_name: Tal - first_name: Jos full_name: Thijssen, Jos last_name: Thijssen - first_name: Michael full_name: Thoss, Michael last_name: Thoss - first_name: Jan M. full_name: van Ruitenbeek, Jan M. last_name: van Ruitenbeek - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 - first_name: David H. full_name: Waldeck, David H. last_name: Waldeck - first_name: Binghai full_name: Yan, Binghai last_name: Yan - first_name: Leeor full_name: Kronik, Leeor last_name: Kronik citation: ama: 'Evers F, Aharony A, Bar‐Gill N, et al. Theory of chirality induced spin selectivity: Progress and challenges. Advanced Materials. 2022;34(13). doi:10.1002/adma.202106629' apa: 'Evers, F., Aharony, A., Bar‐Gill, N., Entin‐Wohlman, O., Hedegård, P., Hod, O., … Kronik, L. (2022). Theory of chirality induced spin selectivity: Progress and challenges. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106629' chicago: 'Evers, Ferdinand, Amnon Aharony, Nir Bar‐Gill, Ora Entin‐Wohlman, Per Hedegård, Oded Hod, Pavel Jelinek, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” Advanced Materials. Wiley, 2022. https://doi.org/10.1002/adma.202106629.' ieee: 'F. Evers et al., “Theory of chirality induced spin selectivity: Progress and challenges,” Advanced Materials, vol. 34, no. 13. Wiley, 2022.' ista: 'Evers F, Aharony A, Bar‐Gill N, Entin‐Wohlman O, Hedegård P, Hod O, Jelinek P, Kamieniarz G, Lemeshko M, Michaeli K, Mujica V, Naaman R, Paltiel Y, Refaely‐Abramson S, Tal O, Thijssen J, Thoss M, van Ruitenbeek JM, Venkataraman L, Waldeck DH, Yan B, Kronik L. 2022. Theory of chirality induced spin selectivity: Progress and challenges. Advanced Materials. 34(13), 2106629.' mla: 'Evers, Ferdinand, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” Advanced Materials, vol. 34, no. 13, 2106629, Wiley, 2022, doi:10.1002/adma.202106629.' short: F. Evers, A. Aharony, N. Bar‐Gill, O. Entin‐Wohlman, P. Hedegård, O. Hod, P. Jelinek, G. Kamieniarz, M. Lemeshko, K. Michaeli, V. Mujica, R. Naaman, Y. Paltiel, S. Refaely‐Abramson, O. Tal, J. Thijssen, M. Thoss, J.M. van Ruitenbeek, L. Venkataraman, D.H. Waldeck, B. Yan, L. Kronik, Advanced Materials 34 (2022). date_created: 2024-09-06T13:07:43Z date_published: 2022-04-01T00:00:00Z date_updated: 2024-12-10T09:43:10Z day: '01' doi: 10.1002/adma.202106629 extern: '1' external_id: arxiv: - '2108.09998' pmid: - '35064943' intvolume: ' 34' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2108.09998 month: '04' oa: 1 oa_version: Preprint pmid: 1 publication: Advanced Materials publication_identifier: issn: - 0935-9648 - 1521-4095 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Theory of chirality induced spin selectivity: Progress and challenges' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2022' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17874' abstract: - lang: eng text: Redox-active two-dimensional polymers (RA-2DPs) are promising lithium battery organic cathode materials due to their regular porosities and high chemical stabilities. However, weak electrical conductivities inherent to the non-conjugated molecular motifs used thus far limit device performance and the practical relevance of these materials. We herein address this problem by developing a modular approach to construct π-conjugated RA-2DPs with a new polycyclic aromatic redox-active building block PDI-DA. Efficient imine-condensation between PDI-DA and two polyfunctional amine nodes followed by quantitative alkyl chain removal produced RA-2DPs TAPPy-PDI and TAPB-PDI as conjugated, porous, polycrystalline networks. In-plane conjugation and permanent porosity endow these materials with high electrical conductivity and high ion diffusion rates. As such, both RA-2DPs function as organic cathode materials with good rate performance and excellent cycling stability. Importantly, the improved design enables higher areal mass-loadings than were previously available, which drives a practical demonstration of TAPPy-PDI as the power source for a series of LED lights. Collectively, this investigation discloses viable synthetic methodologies and design principles for the realization of high-performance organic cathode materials. article_processing_charge: Yes article_type: original author: - first_name: Zexin full_name: Jin, Zexin last_name: Jin - first_name: Qian full_name: Cheng, Qian last_name: Cheng - first_name: Austin M. full_name: Evans, Austin M. last_name: Evans - first_name: Jesse full_name: Gray, Jesse last_name: Gray - first_name: Ruiwen full_name: Zhang, Ruiwen last_name: Zhang - first_name: Si Tong full_name: Bao, Si Tong last_name: Bao - first_name: Fengkai full_name: Wei, Fengkai last_name: Wei - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 - first_name: Yuan full_name: Yang, Yuan last_name: Yang - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls citation: ama: Jin Z, Cheng Q, Evans AM, et al. π-Conjugated redox-active two-dimensional polymers as organic cathode materials. Chemical Science. 2022;13(12):3533-3538. doi:10.1039/d1sc07157b apa: Jin, Z., Cheng, Q., Evans, A. M., Gray, J., Zhang, R., Bao, S. T., … Nuckolls, C. (2022). π-Conjugated redox-active two-dimensional polymers as organic cathode materials. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d1sc07157b chicago: Jin, Zexin, Qian Cheng, Austin M. Evans, Jesse Gray, Ruiwen Zhang, Si Tong Bao, Fengkai Wei, Latha Venkataraman, Yuan Yang, and Colin Nuckolls. “π-Conjugated Redox-Active Two-Dimensional Polymers as Organic Cathode Materials.” Chemical Science. Royal Society of Chemistry, 2022. https://doi.org/10.1039/d1sc07157b. ieee: Z. Jin et al., “π-Conjugated redox-active two-dimensional polymers as organic cathode materials,” Chemical Science, vol. 13, no. 12. Royal Society of Chemistry, pp. 3533–3538, 2022. ista: Jin Z, Cheng Q, Evans AM, Gray J, Zhang R, Bao ST, Wei F, Venkataraman L, Yang Y, Nuckolls C. 2022. π-Conjugated redox-active two-dimensional polymers as organic cathode materials. Chemical Science. 13(12), 3533–3538. mla: Jin, Zexin, et al. “π-Conjugated Redox-Active Two-Dimensional Polymers as Organic Cathode Materials.” Chemical Science, vol. 13, no. 12, Royal Society of Chemistry, 2022, pp. 3533–38, doi:10.1039/d1sc07157b. short: Z. Jin, Q. Cheng, A.M. Evans, J. Gray, R. Zhang, S.T. Bao, F. Wei, L. Venkataraman, Y. Yang, C. Nuckolls, Chemical Science 13 (2022) 3533–3538. date_created: 2024-09-06T13:08:38Z date_published: 2022-03-08T00:00:00Z date_updated: 2024-12-10T09:54:17Z day: '08' doi: 10.1039/d1sc07157b extern: '1' intvolume: ' 13' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/D1SC07157B month: '03' oa: 1 oa_version: Published Version page: 3533-3538 publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: π-Conjugated redox-active two-dimensional polymers as organic cathode materials tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2022' ... --- OA_type: closed access _id: '17875' abstract: - lang: eng text: Nanoscale plasmonic structures have been primarily characterized through scattering studies, but electroluminescence offers an exciting alternative from a technological standpoint by removing the need for optical excitation. In sub-nanometer biased junctions, electronic tunneling can serve as the excitation source for plasmon-coupled electroluminescence, but the gap size dependence to this plasmonic enhancement has not been characterized. Here, we simultaneously probe the electroluminescence and conductance of Au tunnel junctions. We find that plasmonic enhancement increases as the gap size is reduced for junctions biased between 1.4 and 1.8 V, consistent with the behavior of charge transfer plasmons. At biases above 1.9 V, we see decreasing plasmonic enhancement with the decreasing gap, showing quenching due to tunneling in remarkable agreement with the trends observed for high energy plasmons in scattering experiments. Critically, we find that plasmonic enhancement of electroluminescence is gap size-dependent and, furthermore, is in agreement with the nature of modes excited by scattering. article_processing_charge: No article_type: original author: - first_name: Angela L. full_name: Paoletta, Angela L. last_name: Paoletta - first_name: E-Dean full_name: Fung, E-Dean last_name: Fung - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Paoletta AL, Fung E-D, Venkataraman L. Gap size-dependent plasmonic enhancement in electroluminescent tunnel junctions. ACS Photonics. 2022;9(2):688-693. doi:10.1021/acsphotonics.1c01757 apa: Paoletta, A. L., Fung, E.-D., & Venkataraman, L. (2022). Gap size-dependent plasmonic enhancement in electroluminescent tunnel junctions. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.1c01757 chicago: Paoletta, Angela L., E-Dean Fung, and Latha Venkataraman. “Gap Size-Dependent Plasmonic Enhancement in Electroluminescent Tunnel Junctions.” ACS Photonics. American Chemical Society, 2022. https://doi.org/10.1021/acsphotonics.1c01757. ieee: A. L. Paoletta, E.-D. Fung, and L. Venkataraman, “Gap size-dependent plasmonic enhancement in electroluminescent tunnel junctions,” ACS Photonics, vol. 9, no. 2. American Chemical Society, pp. 688–693, 2022. ista: Paoletta AL, Fung E-D, Venkataraman L. 2022. Gap size-dependent plasmonic enhancement in electroluminescent tunnel junctions. ACS Photonics. 9(2), 688–693. mla: Paoletta, Angela L., et al. “Gap Size-Dependent Plasmonic Enhancement in Electroluminescent Tunnel Junctions.” ACS Photonics, vol. 9, no. 2, American Chemical Society, 2022, pp. 688–93, doi:10.1021/acsphotonics.1c01757. short: A.L. Paoletta, E.-D. Fung, L. Venkataraman, ACS Photonics 9 (2022) 688–693. date_created: 2024-09-06T13:09:45Z date_published: 2022-01-14T00:00:00Z date_updated: 2024-12-10T10:01:03Z day: '14' doi: 10.1021/acsphotonics.1c01757 extern: '1' intvolume: ' 9' issue: '2' language: - iso: eng month: '01' oa_version: None page: 688-693 publication: ACS Photonics publication_identifier: issn: - 2330-4022 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Gap size-dependent plasmonic enhancement in electroluminescent tunnel junctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2022' ... --- _id: '18191' abstract: - lang: eng text: 'Large-scale quantum devices provide insights beyond the reach of classical simulations. However, for a reliable and verifiable quantum simulation, the building blocks of the quantum device require exquisite benchmarking. This benchmarking of large-scale dynamical quantum systems represents a major challenge due to lack of efficient tools for their simulation. Here, we present a scalable algorithm based on neural networks for Hamiltonian tomography in out-of-equilibrium quantum systems. We illustrate our approach using a model for a forefront quantum simulation platform: ultracold atoms in optical lattices. Specifically, we show that our algorithm is able to reconstruct the Hamiltonian of an arbitrary sized bosonic ladder system using an accessible amount of experimental measurements. We are able to significantly increase the previously known parameter precision.' article_number: '023302' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Agnes full_name: Valenti, Agnes last_name: Valenti - first_name: Guliuxin full_name: Jin, Guliuxin last_name: Jin - first_name: Julian full_name: Leonard, Julian id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577 last_name: Leonard - first_name: Sebastian D. full_name: Huber, Sebastian D. last_name: Huber - first_name: Eliska full_name: Greplova, Eliska last_name: Greplova citation: ama: Valenti A, Jin G, Leonard J, Huber SD, Greplova E. Scalable Hamiltonian learning for large-scale out-of-equilibrium quantum dynamics. Physical Review A. 2022;105(2). doi:10.1103/physreva.105.023302 apa: Valenti, A., Jin, G., Leonard, J., Huber, S. D., & Greplova, E. (2022). Scalable Hamiltonian learning for large-scale out-of-equilibrium quantum dynamics. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.105.023302 chicago: Valenti, Agnes, Guliuxin Jin, Julian Leonard, Sebastian D. Huber, and Eliska Greplova. “Scalable Hamiltonian Learning for Large-Scale out-of-Equilibrium Quantum Dynamics.” Physical Review A. American Physical Society, 2022. https://doi.org/10.1103/physreva.105.023302. ieee: A. Valenti, G. Jin, J. Leonard, S. D. Huber, and E. Greplova, “Scalable Hamiltonian learning for large-scale out-of-equilibrium quantum dynamics,” Physical Review A, vol. 105, no. 2. American Physical Society, 2022. ista: Valenti A, Jin G, Leonard J, Huber SD, Greplova E. 2022. Scalable Hamiltonian learning for large-scale out-of-equilibrium quantum dynamics. Physical Review A. 105(2), 023302. mla: Valenti, Agnes, et al. “Scalable Hamiltonian Learning for Large-Scale out-of-Equilibrium Quantum Dynamics.” Physical Review A, vol. 105, no. 2, 023302, American Physical Society, 2022, doi:10.1103/physreva.105.023302. short: A. Valenti, G. Jin, J. Leonard, S.D. Huber, E. Greplova, Physical Review A 105 (2022). date_created: 2024-10-07T11:46:53Z date_published: 2022-02-01T00:00:00Z date_updated: 2024-10-08T10:00:23Z day: '01' doi: 10.1103/physreva.105.023302 extern: '1' external_id: arxiv: - '2103.01240' intvolume: ' 105' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2103.01240 month: '02' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Scalable Hamiltonian learning for large-scale out-of-equilibrium quantum dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 105 year: '2022' ... --- _id: '18211' abstract: - lang: eng text: 'Deep neural networks are known to be vulnerable to malicious perturbations. Current methods for improving adversarial robustness make use of either implicit or explicit regularization, with the latter is usually based on adversarial training. Randomized smoothing, the averaging of the classifier outputs over a random distribution centered in the sample, has been shown to guarantee a classifier’s performance subject to bounded perturbations of the input. In this work, we study the application of randomized smoothing to improve performance on unperturbed data and increase robustness to adversarial attacks. We propose to combine smoothing along with adversarial training and randomization approaches, and find that doing so significantly improves the resilience compared to the baseline. We examine our method’s performance on common whitebox (FGSM, PGD) and black-box (transferable attack and NAttack) attacks on CIFAR-10 and CIFAR-100, and determine that for a low number of iterations, smoothing provides a significant performance boost that persists even for perturbations with a high attack norm, . For example, under a PGD-10 attack on CIFAR-10 using Wide-ResNet28-4, we achieve 60.3% accuracy for infinity norm ∞ = 8/255 and 13.1% accuracy for ∞ = 35/255 – outperforming previous art by 3% and 6%, respectively. We achieve nearly twice the accuracy on ∞ = 35/255 and even more so for perturbations with higher infinity norm. A reference implementation of the proposed method is provided. ' article_processing_charge: No article_type: original author: - first_name: Yaniv full_name: Nemcovsky, Yaniv last_name: Nemcovsky - first_name: Evgenii full_name: Zheltonozhskii, Evgenii last_name: Zheltonozhskii - first_name: Chaim full_name: Baskin, Chaim last_name: Baskin - first_name: Brian full_name: Chmiel, Brian last_name: Chmiel - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 - first_name: Avi full_name: Mendelson, Avi last_name: Mendelson citation: ama: Nemcovsky Y, Zheltonozhskii E, Baskin C, Chmiel B, Bronstein AM, Mendelson A. Adversarial robustness via noise injection in smoothed models. Applied Intelligence. 2022;53(8):9483-9498. doi:10.1007/s10489-022-03423-5 apa: Nemcovsky, Y., Zheltonozhskii, E., Baskin, C., Chmiel, B., Bronstein, A. M., & Mendelson, A. (2022). Adversarial robustness via noise injection in smoothed models. Applied Intelligence. Springer Nature. https://doi.org/10.1007/s10489-022-03423-5 chicago: Nemcovsky, Yaniv, Evgenii Zheltonozhskii, Chaim Baskin, Brian Chmiel, Alex M. Bronstein, and Avi Mendelson. “Adversarial Robustness via Noise Injection in Smoothed Models.” Applied Intelligence. Springer Nature, 2022. https://doi.org/10.1007/s10489-022-03423-5. ieee: Y. Nemcovsky, E. Zheltonozhskii, C. Baskin, B. Chmiel, A. M. Bronstein, and A. Mendelson, “Adversarial robustness via noise injection in smoothed models,” Applied Intelligence, vol. 53, no. 8. Springer Nature, pp. 9483–9498, 2022. ista: Nemcovsky Y, Zheltonozhskii E, Baskin C, Chmiel B, Bronstein AM, Mendelson A. 2022. Adversarial robustness via noise injection in smoothed models. Applied Intelligence. 53(8), 9483–9498. mla: Nemcovsky, Yaniv, et al. “Adversarial Robustness via Noise Injection in Smoothed Models.” Applied Intelligence, vol. 53, no. 8, Springer Nature, 2022, pp. 9483–98, doi:10.1007/s10489-022-03423-5. short: Y. Nemcovsky, E. Zheltonozhskii, C. Baskin, B. Chmiel, A.M. Bronstein, A. Mendelson, Applied Intelligence 53 (2022) 9483–9498. date_created: 2024-10-08T12:47:53Z date_published: 2022-08-09T00:00:00Z date_updated: 2024-10-09T11:04:54Z day: '09' doi: 10.1007/s10489-022-03423-5 extern: '1' intvolume: ' 53' issue: '8' language: - iso: eng month: '08' oa_version: None page: 9483-9498 publication: Applied Intelligence publication_identifier: eissn: - 1573-7497 issn: - 0924-669X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Adversarial robustness via noise injection in smoothed models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2022' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18220' abstract: - lang: eng text: Synonymous codons translate into the same amino acid. Although the identity of synonymous codons is often considered inconsequential to the final protein structure, there is mounting evidence for an association between the two. Our study examined this association using regression and classification models, finding that codon sequences predict protein backbone dihedral angles with a lower error than amino acid sequences, and that models trained with true dihedral angles have better classification of synonymous codons given structural information than models trained with random dihedral angles. Using this classification approach, we investigated local codon–codon dependencies and tested whether synonymous codon identity can be predicted more accurately from codon context than amino acid context alone, and most specifically which codon context position carries the most predictive power. article_number: '21968' article_processing_charge: Yes article_type: original author: - first_name: Linor full_name: Ackerman-Schraier, Linor last_name: Ackerman-Schraier - first_name: Aviv A. full_name: Rosenberg, Aviv A. last_name: Rosenberg - first_name: Ailie full_name: Marx, Ailie last_name: Marx - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: Ackerman-Schraier L, Rosenberg AA, Marx A, Bronstein AM. Machine learning approaches demonstrate that protein structures carry information about their genetic coding. Scientific Reports. 2022;12. doi:10.1038/s41598-022-25874-z apa: Ackerman-Schraier, L., Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2022). Machine learning approaches demonstrate that protein structures carry information about their genetic coding. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-25874-z chicago: Ackerman-Schraier, Linor, Aviv A. Rosenberg, Ailie Marx, and Alex M. Bronstein. “Machine Learning Approaches Demonstrate That Protein Structures Carry Information about Their Genetic Coding.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-25874-z. ieee: L. Ackerman-Schraier, A. A. Rosenberg, A. Marx, and A. M. Bronstein, “Machine learning approaches demonstrate that protein structures carry information about their genetic coding,” Scientific Reports, vol. 12. Springer Nature, 2022. ista: Ackerman-Schraier L, Rosenberg AA, Marx A, Bronstein AM. 2022. Machine learning approaches demonstrate that protein structures carry information about their genetic coding. Scientific Reports. 12, 21968. mla: Ackerman-Schraier, Linor, et al. “Machine Learning Approaches Demonstrate That Protein Structures Carry Information about Their Genetic Coding.” Scientific Reports, vol. 12, 21968, Springer Nature, 2022, doi:10.1038/s41598-022-25874-z. short: L. Ackerman-Schraier, A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Reports 12 (2022). date_created: 2024-10-08T12:52:29Z date_published: 2022-12-20T00:00:00Z date_updated: 2024-10-14T09:46:06Z day: '20' doi: 10.1038/s41598-022-25874-z extern: '1' external_id: pmid: - '36539476' intvolume: ' 12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41598-022-25874-z month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: issn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Machine learning approaches demonstrate that protein structures carry information about their genetic coding type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2022' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18221' abstract: - lang: eng text: Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases. article_number: '2815' article_processing_charge: Yes article_type: original author: - first_name: Aviv A. full_name: Rosenberg, Aviv A. last_name: Rosenberg - first_name: Ailie full_name: Marx, Ailie last_name: Marx - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: Rosenberg AA, Marx A, Bronstein AM. Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nature Communications. 2022;13. doi:10.1038/s41467-022-30390-9 apa: Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2022). Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-30390-9 chicago: Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “Codon-Specific Ramachandran Plots Show Amino Acid Backbone Conformation Depends on Identity of the Translated Codon.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30390-9. ieee: A. A. Rosenberg, A. Marx, and A. M. Bronstein, “Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Rosenberg AA, Marx A, Bronstein AM. 2022. Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nature Communications. 13, 2815. mla: Rosenberg, Aviv A., et al. “Codon-Specific Ramachandran Plots Show Amino Acid Backbone Conformation Depends on Identity of the Translated Codon.” Nature Communications, vol. 13, 2815, Springer Nature, 2022, doi:10.1038/s41467-022-30390-9. short: A.A. Rosenberg, A. Marx, A.M. Bronstein, Nature Communications 13 (2022). date_created: 2024-10-08T12:53:01Z date_published: 2022-05-20T00:00:00Z date_updated: 2024-10-14T09:49:02Z day: '20' doi: 10.1038/s41467-022-30390-9 extern: '1' external_id: pmid: - '35595777' intvolume: ' 13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-022-30390-9 month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2022' ... --- OA_place: publisher OA_type: free access _id: '18222' abstract: - lang: eng text: "STUDY QUESTION: What is the accuracy and agreement of embryologists when assessing the implantation probability of blastocysts using time-lapse imaging (TLI), and can it be improved with a data-driven algorithm?\r\n\r\nSUMMARY ANSWER: The overall interobserver agreement of a large panel of embryologists was moderate and prediction accuracy was modest, while the purpose-built artificial intelligence model generally resulted in higher performance metrics.\r\n\r\nWHAT IS KNOWN ALREADY: Previous studies have demonstrated significant interobserver variability amongst embryologists when assessing embryo quality. However, data concerning embryologists’ ability to predict implantation probability using TLI is still lacking. Emerging technologies based on data-driven tools have shown great promise for improving embryo selection and predicting clinical outcomes.\r\n\r\nSTUDY DESIGN, SIZE, DURATION: TLI video files of 136 embryos with known implantation data were retrospectively collected from two clinical sites between 2018 and 2019 for the performance assessment of 36 embryologists and comparison with a deep neural network (DNN).\r\n\r\nPARTICIPANTS/MATERIALS, SETTING, METHODS: We recruited 39 embryologists from 13 different countries. All participants were blinded to clinical outcomes. A total of 136 TLI videos of embryos that reached the blastocyst stage were used for this experiment. Each embryo’s likelihood of successfully implanting was assessed by 36 embryologists, providing implantation probability grades (IPGs) from 1 to 5, where 1 indicates a very low likelihood of implantation and 5 indicates a very high likelihood. Subsequently, three embryologists with over 5 years of experience provided Gardner scores. All 136 blastocysts were categorized into three quality groups based on their Gardner scores. Embryologist predictions were then converted into predictions of implantation (IPG ≥ 3) and no implantation (IPG ≤ 2). Embryologists’ performance and agreement were assessed using Fleiss kappa coefficient. A 10-fold cross-validation DNN was developed to provide IPGs for TLI video files. The model’s performance was compared to that of the embryologists.\r\n\r\nMAIN RESULTS AND THE ROLE OF CHANCE: Logistic regression was employed for the following confounding variables: country of residence, academic level, embryo scoring system, log years of experience and experience using TLI. None were found to have a statistically significant impact on embryologist performance at α = 0.05. The average implantation prediction accuracy for the embryologists was 51.9% for all embryos (N = 136). The average accuracy of the embryologists when assessing top quality and poor quality embryos (according to the Gardner score categorizations) was 57.5% and 57.4%, respectively, and 44.6% for fair quality embryos. Overall interobserver agreement was moderate (κ = 0.56, N = 136). The best agreement was achieved in the poor + top quality group (κ = 0.65, N = 77), while the agreement in the fair quality group was lower (κ = 0.25, N = 59). The DNN showed an overall accuracy rate of 62.5%, with accuracies of 62.2%, 61% and 65.6% for the poor, fair and top quality groups, respectively. The AUC for the DNN was higher than that of the embryologists overall (0.70 DNN vs 0.61 embryologists) as well as in all of the Gardner groups (DNN vs embryologists—Poor: 0.69 vs 0.62; Fair: 0.67 vs 0.53; Top: 0.77 vs 0.54).\r\n\r\nLIMITATIONS, REASONS FOR CAUTION: Blastocyst assessment was performed using video files acquired from time-lapse incubators, where each video contained data from a single focal plane. Clinical data regarding the underlying cause of infertility and endometrial thickness before the transfer was not available, yet may explain implantation failure and lower accuracy of IPGs. Implantation was defined as the presence of a gestational sac, whereas the detection of fetal heartbeat is a more robust marker of embryo viability. The raw data were anonymized to the extent that it was not possible to quantify the number of unique patients and cycles included in the study, potentially masking the effect of bias from a limited patient pool. Furthermore, the lack of demographic data makes it difficult to draw conclusions on how representative the dataset was of the wider population. Finally, embryologists were required to assess the implantation potential, not embryo quality. Although this is not the traditional approach to embryo evaluation, morphology/morphokinetics as a means of assessing embryo quality is believed to be strongly correlated with viability and, for some methods, implantation potential.\r\n\r\nWIDER IMPLICATIONS OF THE FINDINGS: Embryo selection is a key element in IVF success and continues to be a challenge. Improving the predictive ability could assist in optimizing implantation success rates and other clinical outcomes and could minimize the financial and emotional burden on the patient. This study demonstrates moderate agreement rates between embryologists, likely due to the subjective nature of embryo assessment. In particular, we found that average embryologist accuracy and agreement were significantly lower for fair quality embryos when compared with that for top and poor quality embryos. Using data-driven algorithms as an assistive tool may help IVF professionals increase success rates and promote much needed standardization in the IVF clinic. Our results indicate a need for further research regarding technological advancement in this field." article_processing_charge: No article_type: original author: - first_name: Daniel E full_name: Fordham, Daniel E last_name: Fordham - first_name: Dror full_name: Rosentraub, Dror last_name: Rosentraub - first_name: Avital L full_name: Polsky, Avital L last_name: Polsky - first_name: Talia full_name: Aviram, Talia last_name: Aviram - first_name: Yotam full_name: Wolf, Yotam last_name: Wolf - first_name: Oriel full_name: Perl, Oriel last_name: Perl - first_name: Asnat full_name: Devir, Asnat last_name: Devir - first_name: Shahar full_name: Rosentraub, Shahar last_name: Rosentraub - first_name: David H full_name: Silver, David H last_name: Silver - first_name: Yael full_name: Gold Zamir, Yael last_name: Gold Zamir - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 - first_name: Miguel full_name: Lara Lara, Miguel last_name: Lara Lara - first_name: Jara full_name: Ben Nagi, Jara last_name: Ben Nagi - first_name: Adrian full_name: Alvarez, Adrian last_name: Alvarez - first_name: Santiago full_name: Munné, Santiago last_name: Munné citation: ama: 'Fordham DE, Rosentraub D, Polsky AL, et al. Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity? Human Reproduction. 2022;37(10):2275-2290. doi:10.1093/humrep/deac171' apa: 'Fordham, D. E., Rosentraub, D., Polsky, A. L., Aviram, T., Wolf, Y., Perl, O., … Munné, S. (2022). Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity? Human Reproduction. Oxford University Press. https://doi.org/10.1093/humrep/deac171' chicago: 'Fordham, Daniel E, Dror Rosentraub, Avital L Polsky, Talia Aviram, Yotam Wolf, Oriel Perl, Asnat Devir, et al. “Embryologist Agreement When Assessing Blastocyst Implantation Probability: Is Data-Driven Prediction the Solution to Embryo Assessment Subjectivity?” Human Reproduction. Oxford University Press, 2022. https://doi.org/10.1093/humrep/deac171.' ieee: 'D. E. Fordham et al., “Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity?,” Human Reproduction, vol. 37, no. 10. Oxford University Press, pp. 2275–2290, 2022.' ista: 'Fordham DE, Rosentraub D, Polsky AL, Aviram T, Wolf Y, Perl O, Devir A, Rosentraub S, Silver DH, Gold Zamir Y, Bronstein AM, Lara Lara M, Ben Nagi J, Alvarez A, Munné S. 2022. Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity? Human Reproduction. 37(10), 2275–2290.' mla: 'Fordham, Daniel E., et al. “Embryologist Agreement When Assessing Blastocyst Implantation Probability: Is Data-Driven Prediction the Solution to Embryo Assessment Subjectivity?” Human Reproduction, vol. 37, no. 10, Oxford University Press, 2022, pp. 2275–90, doi:10.1093/humrep/deac171.' short: D.E. Fordham, D. Rosentraub, A.L. Polsky, T. Aviram, Y. Wolf, O. Perl, A. Devir, S. Rosentraub, D.H. Silver, Y. Gold Zamir, A.M. Bronstein, M. Lara Lara, J. Ben Nagi, A. Alvarez, S. Munné, Human Reproduction 37 (2022) 2275–2290. date_created: 2024-10-08T12:53:20Z date_published: 2022-10-01T00:00:00Z date_updated: 2024-10-14T09:54:40Z day: '01' doi: 10.1093/humrep/deac171 extern: '1' intvolume: ' 37' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/humrep/deac171 month: '10' oa: 1 oa_version: Published Version page: 2275-2290 publication: Human Reproduction publication_identifier: eissn: - 1460-2350 issn: - 0268-1161 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity?' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2022' ... --- OA_type: closed access _id: '18223' abstract: - lang: eng text: The term silent mutation is commonly used to describe (1) a change in the DNA sequence that does not result in an observable effect on the organism’s phenotype; and (2) a synonymous mutation where the nucleotide change leaves the translated amino acid sequence unchanged. When Christian Anfinsen showed that a folded and active protein could be denatured to lose structure and activity and then subsequently renatured to regain the same structure and activity it appeared that the native, thermodynamically stable, structure of a protein depends only on the amino acid sequence and solution conditions (Anfinsen and Haber 1961). This experiment suggested that, once translated, proteins carry no memory of the genetic sequence and led to one of the most erroneous assumptions in modern science; synonymous codons were long considered silent, a mutation of the type that has no effect on an organism’s phenotype. article_processing_charge: No author: - first_name: Aviv A. full_name: Rosenberg, Aviv A. last_name: Rosenberg - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 - first_name: Ailie full_name: Marx, Ailie last_name: Marx citation: ama: 'Rosenberg AA, Bronstein AM, Marx A. Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease. In: Sauna ZE, Kimchi-Sarfaty C, eds. Single Nucleotide Polymorphisms. Cham: Springer Nature; 2022:37-47. doi:10.1007/978-3-031-05616-1_3' apa: 'Rosenberg, A. A., Bronstein, A. M., & Marx, A. (2022). Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease. In Z. E. Sauna & C. Kimchi-Sarfaty (Eds.), Single Nucleotide Polymorphisms (pp. 37–47). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-05616-1_3' chicago: 'Rosenberg, Aviv A., Alex M. Bronstein, and Ailie Marx. “Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease.” In Single Nucleotide Polymorphisms, edited by Zuben E. Sauna and Chava Kimchi-Sarfaty, 37–47. Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-031-05616-1_3.' ieee: 'A. A. Rosenberg, A. M. Bronstein, and A. Marx, “Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease,” in Single Nucleotide Polymorphisms, Z. E. Sauna and C. Kimchi-Sarfaty, Eds. Cham: Springer Nature, 2022, pp. 37–47.' ista: 'Rosenberg AA, Bronstein AM, Marx A. 2022.Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease. In: Single Nucleotide Polymorphisms. , 37–47.' mla: Rosenberg, Aviv A., et al. “Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease.” Single Nucleotide Polymorphisms, edited by Zuben E. Sauna and Chava Kimchi-Sarfaty, Springer Nature, 2022, pp. 37–47, doi:10.1007/978-3-031-05616-1_3. short: A.A. Rosenberg, A.M. Bronstein, A. Marx, in:, Z.E. Sauna, C. Kimchi-Sarfaty (Eds.), Single Nucleotide Polymorphisms, Springer Nature, Cham, 2022, pp. 37–47. date_created: 2024-10-08T12:53:44Z date_published: 2022-08-10T00:00:00Z date_updated: 2024-10-14T09:58:21Z day: '10' doi: 10.1007/978-3-031-05616-1_3 editor: - first_name: Zuben E. full_name: Sauna, Zuben E. last_name: Sauna - first_name: Chava full_name: Kimchi-Sarfaty, Chava last_name: Kimchi-Sarfaty extern: '1' language: - iso: eng month: '08' oa_version: None page: 37-47 place: Cham publication: Single Nucleotide Polymorphisms publication_identifier: eisbn: - '9783031056161' isbn: - '9783031056147' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- OA_place: repository _id: '18224' abstract: - lang: eng text: Learning from one or few visual examples is one of the key capabilities of humans since early infancy, but is still a significant challenge for modern AI systems. While considerable progress has been achieved in few-shot learning from a few image examples, much less attention has been given to the verbal descriptions that are usually provided to infants when they are presented with a new object. In this paper, we focus on the role of additional semantics that can significantly facilitate few-shot visual learning. Building upon recent advances in few-shot learning with additional semantic information, we demonstrate that further improvements are possible by combining multiple and richer semantics (category labels, attributes, and natural language descriptions). Using these ideas, we offer the community new results on the popular miniImageNet and CUB few-shot benchmarks, comparing favorably to the previous state-of-the-art results for both visual only and visual plus semantics-based approaches. We also performed an ablation study investigating the components and design choices of our approach. Code available on github.com/EliSchwartz/mutiple-semantics. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Eli full_name: Schwartz, Eli last_name: Schwartz - first_name: Leonid full_name: Karlinsky, Leonid last_name: Karlinsky - first_name: Rogerio full_name: Feris, Rogerio last_name: Feris - first_name: Raja full_name: Giryes, Raja last_name: Giryes - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: Schwartz E, Karlinsky L, Feris R, Giryes R, Bronstein AM. Baby steps towards few-shot learning with multiple semantics. Pattern Recognition Letters. 2022;160:142-147. doi:10.1016/j.patrec.2022.06.012 apa: Schwartz, E., Karlinsky, L., Feris, R., Giryes, R., & Bronstein, A. M. (2022). Baby steps towards few-shot learning with multiple semantics. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2022.06.012 chicago: Schwartz, Eli, Leonid Karlinsky, Rogerio Feris, Raja Giryes, and Alex M. Bronstein. “Baby Steps towards Few-Shot Learning with Multiple Semantics.” Pattern Recognition Letters. Elsevier, 2022. https://doi.org/10.1016/j.patrec.2022.06.012. ieee: E. Schwartz, L. Karlinsky, R. Feris, R. Giryes, and A. M. Bronstein, “Baby steps towards few-shot learning with multiple semantics,” Pattern Recognition Letters, vol. 160. Elsevier, pp. 142–147, 2022. ista: Schwartz E, Karlinsky L, Feris R, Giryes R, Bronstein AM. 2022. Baby steps towards few-shot learning with multiple semantics. Pattern Recognition Letters. 160, 142–147. mla: Schwartz, Eli, et al. “Baby Steps towards Few-Shot Learning with Multiple Semantics.” Pattern Recognition Letters, vol. 160, Elsevier, 2022, pp. 142–47, doi:10.1016/j.patrec.2022.06.012. short: E. Schwartz, L. Karlinsky, R. Feris, R. Giryes, A.M. Bronstein, Pattern Recognition Letters 160 (2022) 142–147. date_created: 2024-10-08T12:54:03Z date_published: 2022-08-01T00:00:00Z date_updated: 2024-10-14T10:58:20Z day: '01' doi: 10.1016/j.patrec.2022.06.012 extern: '1' external_id: arxiv: - '1906.01905' intvolume: ' 160' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.01905 month: '08' oa: 1 oa_version: Preprint page: 142-147 publication: Pattern Recognition Letters publication_identifier: issn: - 0167-8655 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Baby steps towards few-shot learning with multiple semantics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 160 year: '2022' ...