--- _id: '14543' abstract: - lang: eng text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. article_processing_charge: No article_type: original author: - first_name: Rauan full_name: Kaiyrzhanov, Rauan last_name: Kaiyrzhanov - first_name: Aboulfazl full_name: Rad, Aboulfazl last_name: Rad - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Aida full_name: Bertoli-Avella, Aida last_name: Bertoli-Avella - first_name: Wouter W full_name: Kallemeijn, Wouter W last_name: Kallemeijn - first_name: Annie full_name: Godwin, Annie last_name: Godwin - first_name: Maha S full_name: Zaki, Maha S last_name: Zaki - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Tracy full_name: Lau, Tracy last_name: Lau - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Stephanie full_name: Efthymiou, Stephanie last_name: Efthymiou - first_name: Ehsan full_name: Ghayoor Karimiani, Ehsan last_name: Ghayoor Karimiani - first_name: Maja full_name: Hempel, Maja last_name: Hempel - first_name: Elizabeth A full_name: Normand, Elizabeth A last_name: Normand - first_name: Sabine full_name: Rudnik-Schöneborn, Sabine last_name: Rudnik-Schöneborn - first_name: Ulrich A full_name: Schatz, Ulrich A last_name: Schatz - first_name: Marc P full_name: Baggelaar, Marc P last_name: Baggelaar - first_name: Muhammad full_name: Ilyas, Muhammad last_name: Ilyas - first_name: Tipu full_name: Sultan, Tipu last_name: Sultan - first_name: Javeria Raza full_name: Alvi, Javeria Raza last_name: Alvi - first_name: Manizha full_name: Ganieva, Manizha last_name: Ganieva - first_name: Ben full_name: Fowler, Ben last_name: Fowler - first_name: Ruxandra full_name: Aanicai, Ruxandra last_name: Aanicai - first_name: Gulsen full_name: Akay Tayfun, Gulsen last_name: Akay Tayfun - first_name: Abdulaziz full_name: Al Saman, Abdulaziz last_name: Al Saman - first_name: Abdulrahman full_name: Alswaid, Abdulrahman last_name: Alswaid - first_name: Nafise full_name: Amiri, Nafise last_name: Amiri - first_name: Nilufar full_name: Asilova, Nilufar last_name: Asilova - first_name: Vorasuk full_name: Shotelersuk, Vorasuk last_name: Shotelersuk - first_name: Patra full_name: Yeetong, Patra last_name: Yeetong - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Meisam full_name: Babaei, Meisam last_name: Babaei - first_name: Gholamreza full_name: Bahrami Monajemi, Gholamreza last_name: Bahrami Monajemi - first_name: Pouria full_name: Mohammadi, Pouria last_name: Mohammadi - first_name: Saeed full_name: Samie, Saeed last_name: Samie - first_name: Selina Husna full_name: Banu, Selina Husna last_name: Banu - first_name: Jorge Pinto full_name: Basto, Jorge Pinto last_name: Basto - first_name: Fanny full_name: Kortüm, Fanny last_name: Kortüm - first_name: Mislen full_name: Bauer, Mislen last_name: Bauer - first_name: Peter full_name: Bauer, Peter last_name: Bauer - first_name: Christian full_name: Beetz, Christian last_name: Beetz - first_name: Masoud full_name: Garshasbi, Masoud last_name: Garshasbi - first_name: Awatif full_name: Hameed Issa, Awatif last_name: Hameed Issa - first_name: Wafaa full_name: Eyaid, Wafaa last_name: Eyaid - first_name: Hind full_name: Ahmed, Hind last_name: Ahmed - first_name: Narges full_name: Hashemi, Narges last_name: Hashemi - first_name: Kazem full_name: Hassanpour, Kazem last_name: Hassanpour - first_name: Isabella full_name: Herman, Isabella last_name: Herman - first_name: Sherozjon full_name: Ibrohimov, Sherozjon last_name: Ibrohimov - first_name: Ban A full_name: Abdul-Majeed, Ban A last_name: Abdul-Majeed - first_name: Maria full_name: Imdad, Maria last_name: Imdad - first_name: Maksudjon full_name: Isrofilov, Maksudjon last_name: Isrofilov - first_name: Qassem full_name: Kaiyal, Qassem last_name: Kaiyal - first_name: Suliman full_name: Khan, Suliman last_name: Khan - first_name: Brian full_name: Kirmse, Brian last_name: Kirmse - first_name: Janet full_name: Koster, Janet last_name: Koster - first_name: Charles Marques full_name: Lourenço, Charles Marques last_name: Lourenço - first_name: Tadahiro full_name: Mitani, Tadahiro last_name: Mitani - first_name: Oana full_name: Moldovan, Oana last_name: Moldovan - first_name: David full_name: Murphy, David last_name: Murphy - first_name: Maryam full_name: Najafi, Maryam last_name: Najafi - first_name: Davut full_name: Pehlivan, Davut last_name: Pehlivan - first_name: Maria Eugenia full_name: Rocha, Maria Eugenia last_name: Rocha - first_name: Vincenzo full_name: Salpietro, Vincenzo last_name: Salpietro - first_name: Miriam full_name: Schmidts, Miriam last_name: Schmidts - first_name: Adel full_name: Shalata, Adel last_name: Shalata - first_name: Mohammad full_name: Mahroum, Mohammad last_name: Mahroum - first_name: Jawabreh Kassem full_name: Talbeya, Jawabreh Kassem last_name: Talbeya - first_name: Robert W full_name: Taylor, Robert W last_name: Taylor - first_name: Dayana full_name: Vazquez, Dayana last_name: Vazquez - first_name: Annalisa full_name: Vetro, Annalisa last_name: Vetro - first_name: Hans R full_name: Waterham, Hans R last_name: Waterham - first_name: Mashaya full_name: Zaman, Mashaya last_name: Zaman - first_name: Tina A full_name: Schrader, Tina A last_name: Schrader - first_name: Wendy K full_name: Chung, Wendy K last_name: Chung - first_name: Renzo full_name: Guerrini, Renzo last_name: Guerrini - first_name: James R full_name: Lupski, James R last_name: Lupski - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson - first_name: Mohnish full_name: Suri, Mohnish last_name: Suri - first_name: Yalda full_name: Jamshidi, Yalda last_name: Jamshidi - first_name: Kailash P full_name: Bhatia, Kailash P last_name: Bhatia - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Michael full_name: Schrader, Michael last_name: Schrader - first_name: Mariasavina full_name: Severino, Mariasavina last_name: Severino - first_name: Matthew full_name: Guille, Matthew last_name: Guille - first_name: Edward W full_name: Tate, Edward W last_name: Tate - first_name: Gaurav K full_name: Varshney, Gaurav K last_name: Varshney - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian citation: ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2024;147(4):1436-1456. doi:10.1093/brain/awad380 apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380 chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2024. https://doi.org/10.1093/brain/awad380. ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain, vol. 147, no. 4. Oxford University Press, pp. 1436–1456, 2024. ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 147(4), 1436–1456. mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, vol. 147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:10.1093/brain/awad380. short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024) 1436–1456. date_created: 2023-11-16T12:36:51Z date_published: 2024-04-01T00:00:00Z date_updated: 2024-07-16T08:23:24Z day: '01' ddc: - '570' department: - _id: GradSch doi: 10.1093/brain/awad380 extern: '1' external_id: pmid: - '37951597' file: - access_level: open_access checksum: 0ee7a8ab9300225d60968f7a3e3cfa0d content_type: application/pdf creator: dernst date_created: 2024-07-16T08:22:13Z date_updated: 2024-07-16T08:22:13Z file_id: '17254' file_name: 2024_Brain_Kaiyrzhanov.pdf file_size: 2641456 relation: main_file success: 1 file_date_updated: 2024-07-16T08:22:13Z fulldoi: https://doi.org/10.1093/brain/awad380 has_accepted_license: '1' intvolume: ' 147' issue: '4' keyword: - Neurology (clinical) language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 1436-1456 pmid: 1 publication: Brain publication_identifier: eissn: - 1460-2156 issn: - 0006-8950 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders 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: 147 year: '2024' ... --- _id: '14726' abstract: - lang: eng text: Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants. article_number: koad324 article_processing_charge: No article_type: original author: - first_name: Liang-Zi full_name: Zhou, Liang-Zi last_name: Zhou - first_name: Lele full_name: Wang, Lele last_name: Wang - first_name: Xia full_name: Chen, Xia last_name: Chen - first_name: Zengxiang full_name: Ge, Zengxiang id: f43371a3-09ff-11eb-8013-bd0c6a2f6de8 last_name: Ge orcid: 0000-0001-9381-3577 - first_name: Julia full_name: Mergner, Julia last_name: Mergner - first_name: Xingli full_name: Li, Xingli last_name: Li - first_name: Bernhard full_name: Küster, Bernhard last_name: Küster - first_name: Gernot full_name: Längst, Gernot last_name: Längst - first_name: Li-Jia full_name: Qu, Li-Jia last_name: Qu - first_name: Thomas full_name: Dresselhaus, Thomas last_name: Dresselhaus citation: ama: Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 2024;36(5). doi:10.1093/plcell/koad324 apa: Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2024). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koad324 chicago: Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell. Oxford University Press, 2024. https://doi.org/10.1093/plcell/koad324. ieee: L.-Z. Zhou et al., “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” The Plant Cell, vol. 36, no. 5. Oxford University Press, 2024. ista: Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2024. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 36(5), koad324. mla: Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell, vol. 36, no. 5, koad324, Oxford University Press, 2024, doi:10.1093/plcell/koad324. short: L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell 36 (2024). date_created: 2024-01-02T11:19:37Z date_published: 2024-05-01T00:00:00Z date_updated: 2024-07-16T11:18:46Z day: '01' ddc: - '580' doi: 10.1093/plcell/koad324 extern: '1' external_id: pmid: - '38142229' fulldoi: https://doi.org/10.1093/plcell/koad324 has_accepted_license: '1' intvolume: ' 36' issue: '5' keyword: - Cell Biology - Plant Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/plcell/koad324 month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize 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: 36 year: '2024' ... --- _id: '15189' abstract: - lang: eng text: Cataclysmic variables (CVs) that have evolved past the period minimum during their lifetimes are predicted to be systems with a brown dwarf donor. While population synthesis models predict that around 40–70 per cent of the Galactic CVs are post-period minimum systems referred to as ‘period bouncers’, only a few dozen confirmed systems are known. We report the study and characterization of a new eclipsing CV, SRGeJ041130.3+685350 (SRGeJ0411), discovered from a joint SRG/eROSITA and ZTF programme. The optical spectrum of SRGeJ0411 shows prominent hydrogen and helium emission lines, typical for CVs. We obtained optical high-speed photometry to confirm the eclipse of SRGeJ0411 and determine the orbital period to be Porb ≈ 97.530 min. The spectral energy distribution suggests that the donor has an effective temperature of ≲ 1800 K. We constrain the donor mass with the period–density relationship for Roche lobe-filling stars and find that Mdonor ≲ 0.04 M⊙. The binary parameters are consistent with evolutionary models for post-period minimum CVs, suggesting that SRGeJ0411 is a new period bouncer. The optical emission lines of SRGeJ0411 are single-peaked despite the system being eclipsing, which is typically only seen due to stream-fed accretion in polars. X-ray spectroscopy hints that the white dwarf in SRGeJ0411 could be magnetic, but verifying the magnetic nature of SRGeJ0411 requires further investigation. The lack of optical outbursts has made SRGeJ0411 elusive in previous surveys, and joint X-ray and optical surveys highlight the potential for discovering similar systems in the near future. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Ilkham full_name: Galiullin, Ilkham last_name: Galiullin - first_name: Antonio C full_name: Rodriguez, Antonio C last_name: Rodriguez - first_name: Shrinivas R full_name: Kulkarni, Shrinivas R last_name: Kulkarni - first_name: Rashid full_name: Sunyaev, Rashid last_name: Sunyaev - first_name: Marat full_name: Gilfanov, Marat last_name: Gilfanov - first_name: Ilfan full_name: Bikmaev, Ilfan last_name: Bikmaev - first_name: Lev full_name: Yungelson, Lev last_name: Yungelson - first_name: Jan full_name: van Roestel, Jan last_name: van Roestel - first_name: Boris T full_name: Gänsicke, Boris T last_name: Gänsicke - first_name: Irek full_name: Khamitov, Irek last_name: Khamitov - first_name: Paula full_name: Szkody, Paula last_name: Szkody - first_name: Kareem full_name: El-Badry, Kareem last_name: El-Badry - first_name: Mikhail full_name: Suslikov, Mikhail last_name: Suslikov - first_name: Thomas A full_name: Prince, Thomas A last_name: Prince - first_name: Mikhail full_name: Buntov, Mikhail last_name: Buntov - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Mark full_name: Gorbachev, Mark last_name: Gorbachev - first_name: Matthew J full_name: Graham, Matthew J last_name: Graham - first_name: Rustam full_name: Gumerov, Rustam last_name: Gumerov - first_name: Eldar full_name: Irtuganov, Eldar last_name: Irtuganov - first_name: Russ R full_name: Laher, Russ R last_name: Laher - first_name: Pavel full_name: Medvedev, Pavel last_name: Medvedev - first_name: Reed full_name: Riddle, Reed last_name: Riddle - first_name: Ben full_name: Rusholme, Ben last_name: Rusholme - first_name: Nail full_name: Sakhibullin, Nail last_name: Sakhibullin - first_name: Alexander full_name: Sklyanov, Alexander last_name: Sklyanov - first_name: Zachary P full_name: Vanderbosch, Zachary P last_name: Vanderbosch citation: ama: 'Galiullin I, Rodriguez AC, Kulkarni SR, et al. A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary. Monthly Notices of the Royal Astronomical Society. 2024;528(1):676-692. doi:10.1093/mnras/stae012' apa: 'Galiullin, I., Rodriguez, A. C., Kulkarni, S. R., Sunyaev, R., Gilfanov, M., Bikmaev, I., … Vanderbosch, Z. P. (2024). A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae012' chicago: 'Galiullin, Ilkham, Antonio C Rodriguez, Shrinivas R Kulkarni, Rashid Sunyaev, Marat Gilfanov, Ilfan Bikmaev, Lev Yungelson, et al. “A Joint SRG/EROSITA + ZTF Search: Discovery of a 97-Min Period Eclipsing Cataclysmic Variable with Evidence of a Brown Dwarf Secondary.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae012.' ieee: 'I. Galiullin et al., “A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary,” Monthly Notices of the Royal Astronomical Society, vol. 528, no. 1. Oxford University Press, pp. 676–692, 2024.' ista: 'Galiullin I, Rodriguez AC, Kulkarni SR, Sunyaev R, Gilfanov M, Bikmaev I, Yungelson L, van Roestel J, Gänsicke BT, Khamitov I, Szkody P, El-Badry K, Suslikov M, Prince TA, Buntov M, Caiazzo I, Gorbachev M, Graham MJ, Gumerov R, Irtuganov E, Laher RR, Medvedev P, Riddle R, Rusholme B, Sakhibullin N, Sklyanov A, Vanderbosch ZP. 2024. A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary. Monthly Notices of the Royal Astronomical Society. 528(1), 676–692.' mla: 'Galiullin, Ilkham, et al. “A Joint SRG/EROSITA + ZTF Search: Discovery of a 97-Min Period Eclipsing Cataclysmic Variable with Evidence of a Brown Dwarf Secondary.” Monthly Notices of the Royal Astronomical Society, vol. 528, no. 1, Oxford University Press, 2024, pp. 676–92, doi:10.1093/mnras/stae012.' short: I. Galiullin, A.C. Rodriguez, S.R. Kulkarni, R. Sunyaev, M. Gilfanov, I. Bikmaev, L. Yungelson, J. van Roestel, B.T. Gänsicke, I. Khamitov, P. Szkody, K. El-Badry, M. Suslikov, T.A. Prince, M. Buntov, I. Caiazzo, M. Gorbachev, M.J. Graham, R. Gumerov, E. Irtuganov, R.R. Laher, P. Medvedev, R. Riddle, B. Rusholme, N. Sakhibullin, A. Sklyanov, Z.P. Vanderbosch, Monthly Notices of the Royal Astronomical Society 528 (2024) 676–692. date_created: 2024-03-26T09:43:55Z date_published: 2024-01-04T00:00:00Z date_updated: 2024-04-02T06:50:01Z day: '04' doi: 10.1093/mnras/stae012 extern: '1' external_id: arxiv: - '2401.04178' fulldoi: https://doi.org/10.1093/mnras/stae012 intvolume: ' 528' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stae012 month: '01' oa: 1 oa_version: Published Version page: 676-692 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary' 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: 528 year: '2024' ... --- _id: '15191' abstract: - lang: eng text: Despite their shared origin, members of globular clusters display star-to-star variations in composition. The observed pattern of element abundances is unique to these stellar environments and cannot be fully explained by any proposed mechanism. It remains unclear whether stars form with chemical heterogeneity or inherit it from interactions with other members. These scenarios may be differentiated by the dependence of chemical spread on stellar mass; however, obtaining a sufficiently large mass baseline requires abundance measurements on the lower main sequence, which is too faint for spectroscopy even in the nearest globular clusters. We developed a stellar modeling method to obtain precise chemical abundances for stars near the end of the main sequence from multiband photometry, and we applied it to the globular cluster 47 Tucanae. The computational efficiency is attained by matching chemical elements to the model components that are most sensitive to their abundance. We determined [O/Fe] for ∼5000 members below the main-sequence knee at the level of accuracy, comparable to the spectroscopic measurements of evolved members in the literature. The inferred distribution disfavors stellar interactions as the origin of chemical spread; however, an accurate theory of accretion is required to draw a more definitive conclusion. We anticipate that future observations of 47 Tucanae with the James Webb Space Telescope will extend the mass baseline of our analysis into the substellar regime. Therefore, we present predicted color–magnitude diagrams and mass–magnitude relations for the brown dwarf members of 47 Tucanae. article_number: '139' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Roman full_name: Gerasimov, Roman last_name: Gerasimov - first_name: Adam J. full_name: Burgasser, Adam J. last_name: Burgasser - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Derek full_name: Homeier, Derek last_name: Homeier - first_name: Harvey B. full_name: Richer, Harvey B. last_name: Richer - first_name: Matteo full_name: Correnti, Matteo last_name: Correnti - first_name: Jeremy full_name: Heyl, Jeremy last_name: Heyl citation: ama: Gerasimov R, Burgasser AJ, Caiazzo I, et al. Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams. The Astrophysical Journal. 2024;961(1). doi:10.3847/1538-4357/ad08bf apa: Gerasimov, R., Burgasser, A. J., Caiazzo, I., Homeier, D., Richer, H. B., Correnti, M., & Heyl, J. (2024). Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad08bf chicago: Gerasimov, Roman, Adam J. Burgasser, Ilaria Caiazzo, Derek Homeier, Harvey B. Richer, Matteo Correnti, and Jeremy Heyl. “Exploring the Chemistry and Mass Function of the Globular Cluster 47 Tucanae with New Theoretical Color–Magnitude Diagrams.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad08bf. ieee: R. Gerasimov et al., “Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams,” The Astrophysical Journal, vol. 961, no. 1. American Astronomical Society, 2024. ista: Gerasimov R, Burgasser AJ, Caiazzo I, Homeier D, Richer HB, Correnti M, Heyl J. 2024. Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams. The Astrophysical Journal. 961(1), 139. mla: Gerasimov, Roman, et al. “Exploring the Chemistry and Mass Function of the Globular Cluster 47 Tucanae with New Theoretical Color–Magnitude Diagrams.” The Astrophysical Journal, vol. 961, no. 1, 139, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad08bf. short: R. Gerasimov, A.J. Burgasser, I. Caiazzo, D. Homeier, H.B. Richer, M. Correnti, J. Heyl, The Astrophysical Journal 961 (2024). date_created: 2024-03-26T09:44:50Z date_published: 2024-01-22T00:00:00Z date_updated: 2024-04-02T06:52:43Z day: '22' doi: 10.3847/1538-4357/ad08bf extern: '1' external_id: arxiv: - '2310.11800' fulldoi: https://doi.org/10.3847/1538-4357/ad08bf intvolume: ' 961' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3847/1538-4357/ad08bf month: '01' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams 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: 961 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '15379' abstract: - lang: eng text: Long-term potentiation (LTP) of excitatory synapses is a leading model to explain the concept of information storage in the brain. Multiple mechanisms contribute to LTP, but central amongst them is an increased sensitivity of the postsynaptic membrane to neurotransmitter release. This sensitivity is predominantly determined by the abundance and localization of AMPA-type glutamate receptors (AMPARs). A combination of AMPAR structural data, super-resolution imaging of excitatory synapses, and an abundance of electrophysiological studies are providing an ever-clearer picture of how AMPARs are recruited and organized at synaptic junctions. Here, we review the latest insights into this process, and discuss how both cytoplasmic and extracellular receptor elements cooperate to tune the AMPAR response at the hippocampal CA1 synapse. acknowledgement: The authors thank Alexander Scrutton and James M. Krieger for comments on the manuscript. The authors also acknowledge Shraddha Nayak for help with Figure 1B design. This work was supported by grants from the Medical Research Council (MC_U105174197), the BBSRC (BB/N002113/1), and the Wellcome Trust (223194/Z/21/Z) to IHG. article_number: ' 2400006' article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Imogen full_name: Stockwell, Imogen last_name: Stockwell - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Ingo H. full_name: Greger, Ingo H. last_name: Greger citation: ama: Stockwell I, Watson J, Greger IH. Tuning synaptic strength by regulation of AMPA glutamate receptor localization. BioEssays. 2024;46(7). doi:10.1002/bies.202400006 apa: Stockwell, I., Watson, J., & Greger, I. H. (2024). Tuning synaptic strength by regulation of AMPA glutamate receptor localization. BioEssays. Wiley. https://doi.org/10.1002/bies.202400006 chicago: Stockwell, Imogen, Jake Watson, and Ingo H. Greger. “Tuning Synaptic Strength by Regulation of AMPA Glutamate Receptor Localization.” BioEssays. Wiley, 2024. https://doi.org/10.1002/bies.202400006. ieee: I. Stockwell, J. Watson, and I. H. Greger, “Tuning synaptic strength by regulation of AMPA glutamate receptor localization,” BioEssays, vol. 46, no. 7. Wiley, 2024. ista: Stockwell I, Watson J, Greger IH. 2024. Tuning synaptic strength by regulation of AMPA glutamate receptor localization. BioEssays. 46(7), 2400006. mla: Stockwell, Imogen, et al. “Tuning Synaptic Strength by Regulation of AMPA Glutamate Receptor Localization.” BioEssays, vol. 46, no. 7, 2400006, Wiley, 2024, doi:10.1002/bies.202400006. short: I. Stockwell, J. Watson, I.H. Greger, BioEssays 46 (2024). date_created: 2024-05-12T22:01:02Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T07:25:02Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1002/bies.202400006 external_id: isi: - '001214545700001' pmid: - '38693811' file: - access_level: open_access checksum: dc8be74156657e8aab12a9d613233ee3 content_type: application/pdf creator: dernst date_created: 2025-01-09T09:31:05Z date_updated: 2025-01-09T09:31:05Z file_id: '18801' file_name: 2024_BioEssays_Stockwell.pdf file_size: 775825 relation: main_file success: 1 file_date_updated: 2025-01-09T09:31:05Z fulldoi: https://doi.org/10.1002/bies.202400006 has_accepted_license: '1' intvolume: ' 46' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: BioEssays publication_identifier: eissn: - 1521-1878 issn: - 0265-9247 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Tuning synaptic strength by regulation of AMPA glutamate receptor localization 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 46 year: '2024' ... --- _id: '17042' abstract: - lang: eng text: 'Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13C-13C and heteronuclear H-N, H-C and N-C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples. ' article_processing_charge: No author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Schanda P. Raw data to “MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” 2024. doi:10.15479/AT:ISTA:17042' apa: 'Schanda, P. (2024). Raw data to “MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17042' chicago: 'Schanda, Paul. “Raw Data to ‘MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17042.' ieee: 'P. Schanda, “Raw data to ‘MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.’” Institute of Science and Technology Austria, 2024.' ista: 'Schanda P. 2024. Raw data to ‘MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17042.' mla: 'Schanda, Paul. Raw Data to “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17042.' short: P. Schanda, (2024). contributor: - contributor_type: data_collector first_name: Alicia last_name: Vallet - contributor_type: data_collector first_name: 'Isabel ' last_name: Ayala - contributor_type: data_collector first_name: Barbara last_name: Perrone - contributor_type: data_collector first_name: Alia last_name: Hassan - contributor_type: data_collector first_name: Catherine last_name: Bougault corr_author: '1' date_created: 2024-05-22T12:04:54Z date_published: 2024-05-22T00:00:00Z date_updated: 2025-09-09T12:01:41Z day: '22' ddc: - '570' department: - _id: PaSc doi: 10.15479/AT:ISTA:17042 file: - access_level: open_access checksum: eb55f0988342d927702353b75e07edfa content_type: text/plain creator: pschanda date_created: 2024-05-22T12:05:13Z date_updated: 2024-05-22T12:05:13Z file_id: '17043' file_name: Read_me.txt file_size: 2132 relation: main_file success: 1 - access_level: open_access checksum: 3393592acaf5ee1e032052c236780914 content_type: application/zip creator: pschanda date_created: 2024-05-22T12:17:10Z date_updated: 2024-05-22T12:17:10Z file_id: '17044' file_name: raw_data_CryoMAS_cyronebacteria.zip file_size: 755704888 relation: main_file success: 1 file_date_updated: 2024-05-22T12:17:10Z fulldoi: https://doi.org/10.15479/AT:ISTA:17042 has_accepted_license: '1' keyword: - nuclear magnetic resonance - NMR - cellwall - structural biology - spectroscopy month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '17291' relation: used_in_publication status: public status: public title: 'Raw data to "MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments"' 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '17111' abstract: - lang: eng text: Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets. article_processing_charge: No article_type: original author: - first_name: Advika full_name: Kamatar, Advika last_name: Kamatar - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Feng full_name: Yuan, Feng last_name: Yuan - first_name: Liping full_name: Wang, Liping last_name: Wang - first_name: Eileen M. full_name: Lafer, Eileen M. last_name: Lafer - first_name: David W. full_name: Taylor, David W. last_name: Taylor - first_name: Jeanne C. full_name: Stachowiak, Jeanne C. last_name: Stachowiak - first_name: Sapun H. full_name: Parekh, Sapun H. last_name: Parekh citation: ama: Kamatar A, Bravo JPK, Yuan F, et al. Lipid droplets as substrates for protein phase separation. Biophysical Journal. 2024;123(11):1494-1507. doi:10.1016/j.bpj.2024.03.015 apa: Kamatar, A., Bravo, J. P. K., Yuan, F., Wang, L., Lafer, E. M., Taylor, D. W., … Parekh, S. H. (2024). Lipid droplets as substrates for protein phase separation. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2024.03.015 chicago: Kamatar, Advika, Jack Peter Kelly Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, and Sapun H. Parekh. “Lipid Droplets as Substrates for Protein Phase Separation.” Biophysical Journal. Elsevier, 2024. https://doi.org/10.1016/j.bpj.2024.03.015. ieee: A. Kamatar et al., “Lipid droplets as substrates for protein phase separation,” Biophysical Journal, vol. 123, no. 11. Elsevier, pp. 1494–1507, 2024. ista: Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC, Parekh SH. 2024. Lipid droplets as substrates for protein phase separation. Biophysical Journal. 123(11), 1494–1507. mla: Kamatar, Advika, et al. “Lipid Droplets as Substrates for Protein Phase Separation.” Biophysical Journal, vol. 123, no. 11, Elsevier, 2024, pp. 1494–507, doi:10.1016/j.bpj.2024.03.015. short: A. Kamatar, J.P.K. Bravo, F. Yuan, L. Wang, E.M. Lafer, D.W. Taylor, J.C. Stachowiak, S.H. Parekh, Biophysical Journal 123 (2024) 1494–1507. date_created: 2024-06-04T06:41:03Z date_published: 2024-06-04T00:00:00Z date_updated: 2025-01-13T11:03:41Z day: '04' doi: 10.1016/j.bpj.2024.03.015 extern: '1' external_id: pmid: - '38462838' fulldoi: https://doi.org/10.1016/j.bpj.2024.03.015 intvolume: ' 123' issue: '11' language: - iso: eng month: '06' oa_version: None page: 1494-1507 pmid: 1 publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Lipid droplets as substrates for protein phase separation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 123 year: '2024' ... --- OA_place: repository OA_type: green _id: '17112' abstract: - lang: eng text: The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities. acknowledgement: We thank R. Fregoso Ocampo for assistance with negative-stain EM imaging. This work was funded by Dutch Research Council (NWO) VIDI grant VI.Vidi.203.074 (R.H.J.S.), NWO Spinoza grant SPI 93-537 (J.v.d.O.), European Research Council (ERC) Advanced grant ERC-AdG-834279 (J.v.d.O.), ERC CoG grant 817834 (T.J.G.E.), NWO VICI grant VI.C.192.016 (T.J.G.E.), Volkswagen Foundation grant 96725 (T.J.G.E.), National Institute of General Medical Sciences of the National Institutes of Health grant R35GM138348 (D.W.T.), Welch Foundation research grant F-1938 (D.W.T.), a Robert J. Kleberg, Jr. And Helen C. Kleberg Foundation medical research grant (D.W.T.), and American Cancer Society Research Scholar grant RSG-21-050-01-DMC (D.W.T.). article_processing_charge: No article_type: original author: - first_name: Jurre A. full_name: Steens, Jurre A. last_name: Steens - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Carl Raymund P. full_name: Salazar, Carl Raymund P. last_name: Salazar - first_name: Caglar full_name: Yildiz, Caglar last_name: Yildiz - first_name: Afonso M. full_name: Amieiro, Afonso M. last_name: Amieiro - first_name: Stephan full_name: Köstlbacher, Stephan last_name: Köstlbacher - first_name: Stijn H.P. full_name: Prinsen, Stijn H.P. last_name: Prinsen - first_name: Constantinos full_name: Patinios, Constantinos last_name: Patinios - first_name: Andreas full_name: Bardis, Andreas last_name: Bardis - first_name: Arjan full_name: Barendregt, Arjan last_name: Barendregt - first_name: Richard A. full_name: Scheltema, Richard A. last_name: Scheltema - first_name: Thijs J.G. full_name: Ettema, Thijs J.G. last_name: Ettema - first_name: John full_name: van der Oost, John last_name: van der Oost - first_name: David W. full_name: Taylor, David W. last_name: Taylor - first_name: Raymond H.J. full_name: Staals, Raymond H.J. last_name: Staals citation: ama: Steens JA, Bravo JPK, Salazar CRP, et al. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science. 2024;383(6682):512-519. doi:10.1126/science.adk0378 apa: Steens, J. A., Bravo, J. P. K., Salazar, C. R. P., Yildiz, C., Amieiro, A. M., Köstlbacher, S., … Staals, R. H. J. (2024). Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adk0378 chicago: Steens, Jurre A., Jack Peter Kelly Bravo, Carl Raymund P. Salazar, Caglar Yildiz, Afonso M. Amieiro, Stephan Köstlbacher, Stijn H.P. Prinsen, et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adk0378. ieee: J. A. Steens et al., “Type III-B CRISPR-Cas cascade of proteolytic cleavages,” Science, vol. 383, no. 6682. American Association for the Advancement of Science, pp. 512–519, 2024. ista: Steens JA, Bravo JPK, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen SHP, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJG, van der Oost J, Taylor DW, Staals RHJ. 2024. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science. 383(6682), 512–519. mla: Steens, Jurre A., et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” Science, vol. 383, no. 6682, American Association for the Advancement of Science, 2024, pp. 512–19, doi:10.1126/science.adk0378. short: J.A. Steens, J.P.K. Bravo, C.R.P. Salazar, C. Yildiz, A.M. Amieiro, S. Köstlbacher, S.H.P. Prinsen, C. Patinios, A. Bardis, A. Barendregt, R.A. Scheltema, T.J.G. Ettema, J. van der Oost, D.W. Taylor, R.H.J. Staals, Science 383 (2024) 512–519. date_created: 2024-06-04T06:41:26Z date_published: 2024-02-01T00:00:00Z date_updated: 2025-09-24T08:31:45Z day: '01' doi: 10.1126/science.adk0378 extern: '1' external_id: pmid: - '38301007' fulldoi: https://doi.org/10.1126/science.adk0378 intvolume: ' 383' issue: '6682' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.06.23.546230 month: '02' oa: 1 oa_version: Preprint page: 512-519 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Type III-B CRISPR-Cas cascade of proteolytic cleavages type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 383 year: '2024' ... --- _id: '17113' abstract: - lang: eng text: CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing. article_number: '3663' article_processing_charge: Yes article_type: original author: - first_name: Grace N. full_name: Hibshman, Grace N. last_name: Hibshman - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Matthew M. full_name: Hooper, Matthew M. last_name: Hooper - first_name: Tyler L. full_name: Dangerfield, Tyler L. last_name: Dangerfield - first_name: Hongshan full_name: Zhang, Hongshan last_name: Zhang - first_name: Ilya J. full_name: Finkelstein, Ilya J. last_name: Finkelstein - first_name: Kenneth A. full_name: Johnson, Kenneth A. last_name: Johnson - first_name: David W. full_name: Taylor, David W. last_name: Taylor citation: ama: Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 2024;15. doi:10.1038/s41467-024-47830-3 apa: Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang, H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-47830-3 chicago: Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47830-3. ieee: G. N. Hibshman et al., “Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 15, 3663. mla: Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” Nature Communications, vol. 15, 3663, Springer Nature, 2024, doi:10.1038/s41467-024-47830-3. short: G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J. Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024). date_created: 2024-06-04T06:42:07Z date_published: 2024-04-30T00:00:00Z date_updated: 2024-10-14T12:34:26Z day: '30' doi: 10.1038/s41467-024-47830-3 extern: '1' external_id: pmid: - '38688943' fulldoi: https://doi.org/10.1038/s41467-024-47830-3 intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-024-47830-3 month: '04' 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: Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2024' ... --- _id: '17114' abstract: - lang: eng text: CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction1–5. Target RNA cleavage at regular intervals is characteristic of type III effector complexes6–8. Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors9,10, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes. article_number: '3324' article_processing_charge: Yes article_type: original author: - first_name: Evan A. full_name: Schwartz, Evan A. last_name: Schwartz - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Mohd full_name: Ahsan, Mohd last_name: Ahsan - first_name: Luis A. full_name: Macias, Luis A. last_name: Macias - first_name: Caitlyn L. full_name: McCafferty, Caitlyn L. last_name: McCafferty - first_name: Tyler L. full_name: Dangerfield, Tyler L. last_name: Dangerfield - first_name: Jada N. full_name: Walker, Jada N. last_name: Walker - first_name: Jennifer S. full_name: Brodbelt, Jennifer S. last_name: Brodbelt - first_name: Giulia full_name: Palermo, Giulia last_name: Palermo - first_name: Peter C. full_name: Fineran, Peter C. last_name: Fineran - first_name: Robert D. full_name: Fagerlund, Robert D. last_name: Fagerlund - first_name: David W. full_name: Taylor, David W. last_name: Taylor citation: ama: Schwartz EA, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 2024;15. doi:10.1038/s41467-024-47506-y apa: Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-47506-y chicago: Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47506-y. ieee: E. A. Schwartz et al., “RNA targeting and cleavage by the type III-Dv CRISPR effector complex,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 15, 3324. mla: Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” Nature Communications, vol. 15, 3324, Springer Nature, 2024, doi:10.1038/s41467-024-47506-y. short: E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 15 (2024). date_created: 2024-06-04T06:43:02Z date_published: 2024-04-18T00:00:00Z date_updated: 2024-06-04T07:05:26Z day: '18' doi: 10.1038/s41467-024-47506-y extern: '1' external_id: pmid: - '38637512' fulldoi: https://doi.org/10.1038/s41467-024-47506-y intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-024-47506-y month: '04' 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: RNA targeting and cleavage by the type III-Dv CRISPR effector complex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2024' ... --- _id: '17122' abstract: - lang: eng text: "Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.\r\nMethods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.\r\nResults: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).\r\nConclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses." acknowledgement: "This work was supported by the project ‘Fellows Ride’ of the Thomas Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’ (to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL." article_number: '401' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Hannah full_name: Ramming, Hannah last_name: Ramming - first_name: Linda full_name: Theuerkauf, Linda last_name: Theuerkauf - first_name: Olaf full_name: Hoos, Olaf last_name: Hoos - first_name: Katharina full_name: Lichter, Katharina id: 39302e62-fcfc-11ec-8196-8b01447dbd3d last_name: Lichter orcid: 0000-0002-1485-0351 - first_name: Sarah full_name: Kittel-Schneider, Sarah last_name: Kittel-Schneider citation: ama: Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. 2024;24. doi:10.1186/s12888-024-05849-2 apa: Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., & Kittel-Schneider, S. (2024). The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. Springer Nature. https://doi.org/10.1186/s12888-024-05849-2 chicago: Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” BMC Psychiatry. Springer Nature, 2024. https://doi.org/10.1186/s12888-024-05849-2. ieee: H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study,” BMC Psychiatry, vol. 24. Springer Nature, 2024. ista: Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. 24, 401. mla: Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” BMC Psychiatry, vol. 24, 401, Springer Nature, 2024, doi:10.1186/s12888-024-05849-2. short: H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC Psychiatry 24 (2024). date_created: 2024-06-09T22:01:01Z date_published: 2024-05-29T00:00:00Z date_updated: 2025-04-23T07:51:51Z day: '29' ddc: - '570' department: - _id: PeJo doi: 10.1186/s12888-024-05849-2 external_id: pmid: - '38811916' file: - access_level: open_access checksum: 5df60d3c9388955c5b682ea34748d59d content_type: application/pdf creator: dernst date_created: 2024-06-10T10:44:26Z date_updated: 2024-06-10T10:44:26Z file_id: '17131' file_name: 2024_BMCPsychiatry_Ramming.pdf file_size: 2320147 relation: main_file success: 1 file_date_updated: 2024-06-10T10:44:26Z fulldoi: https://doi.org/10.1186/s12888-024-05849-2 has_accepted_license: '1' intvolume: ' 24' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Psychiatry publication_identifier: eissn: - 1471-244X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study 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: '2024' ... --- _id: '17139' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Waleed full_name: Khalid, Waleed id: 097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1 last_name: Khalid - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante - first_name: Stephan full_name: Stadlbauer, Stephan id: 4D0BC184-F248-11E8-B48F-1D18A9856A87 last_name: Stadlbauer citation: ama: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core is requested? In: ASHPC24 - Austrian-Slovenian HPC Meeting 2024. EuroCC Austria; 2024:46. doi:10.25365/phaidra.463' apa: 'Schlögl, A., Khalid, W., Elefante, S., & Stadlbauer, S. (2024). How much memory per CPU core is requested? In ASHPC24 - Austrian-Slovenian HPC Meeting 2024 (p. 46). Grundlsee, Austria: EuroCC Austria. https://doi.org/10.25365/phaidra.463' chicago: Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer. “How Much Memory per CPU Core Is Requested?” In ASHPC24 - Austrian-Slovenian HPC Meeting 2024, 46. EuroCC Austria, 2024. https://doi.org/10.25365/phaidra.463. ieee: A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per CPU core is requested?,” in ASHPC24 - Austrian-Slovenian HPC Meeting 2024, Grundlsee, Austria, 2024, p. 46. ista: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian HPC Meeting, 46.' mla: Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46, doi:10.25365/phaidra.463. short: A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46. conference: end_date: 2024-06-13 location: Grundlsee, Austria name: 'ASHPC: Austrian-Slovenian HPC Meeting' start_date: 2024-06-10 date_created: 2024-06-14T09:06:36Z date_published: 2024-06-13T00:00:00Z date_updated: 2024-06-17T09:40:37Z day: '13' ddc: - '000' department: - _id: ScienComp doi: 10.25365/phaidra.463 file: - access_level: open_access checksum: f7d3dded6df2dcdb4818904cf2e1c183 content_type: application/pdf creator: dernst date_created: 2024-06-17T09:36:51Z date_updated: 2024-06-17T09:36:51Z file_id: '17153' file_name: 2024_ASHPC_Schloegl.pdf file_size: 206746 relation: main_file success: 1 file_date_updated: 2024-06-17T09:36:51Z fulldoi: https://doi.org/10.25365/phaidra.463 has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '46' publication: ASHPC24 - Austrian-Slovenian HPC Meeting 2024 publication_identifier: isbn: - '9783200096455' publication_status: published publisher: EuroCC Austria quality_controlled: '1' status: public title: How much memory per CPU core is requested? 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: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18451' abstract: - lang: eng text: Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials. acknowledgement: This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 101002258). The authors acknowledge the provision of facilities and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence (2022–2029), project number 346110 and 346112. article_number: '2408416' article_processing_charge: Yes article_type: original author: - first_name: Yu full_name: Zhou, Yu last_name: Zhou - first_name: Ahmed full_name: Shaukat, Ahmed last_name: Shaukat - first_name: Jani full_name: Seitsonen, Jani last_name: Seitsonen - first_name: Carlo full_name: Rigoni, Carlo id: c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0 last_name: Rigoni - first_name: Jaakko V.I. full_name: Timonen, Jaakko V.I. last_name: Timonen - first_name: Mauri A. full_name: Kostiainen, Mauri A. last_name: Kostiainen citation: ama: Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 2024;11(45). doi:10.1002/advs.202408416 apa: Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., & Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. Wiley. https://doi.org/10.1002/advs.202408416 chicago: Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen, and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” Advanced Science. Wiley, 2024. https://doi.org/10.1002/advs.202408416. ieee: Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A. Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,” Advanced Science, vol. 11, no. 45. Wiley, 2024. ista: Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 11(45), 2408416. mla: Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” Advanced Science, vol. 11, no. 45, 2408416, Wiley, 2024, doi:10.1002/advs.202408416. short: Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen, Advanced Science 11 (2024). date_created: 2024-10-20T22:02:07Z date_published: 2024-12-04T00:00:00Z date_updated: 2025-09-08T14:20:31Z day: '04' ddc: - '540' department: - _id: RaKl doi: 10.1002/advs.202408416 external_id: isi: - '001330745600001' pmid: - '39401426' file: - access_level: open_access checksum: 00451eeb2c9eecf1ff41ad243c793a51 content_type: application/pdf creator: dernst date_created: 2025-01-13T09:16:25Z date_updated: 2025-01-13T09:16:25Z file_id: '18834' file_name: 2024_AdvancedScience_Zhou.pdf file_size: 7040083 relation: main_file success: 1 file_date_updated: 2025-01-13T09:16:25Z fulldoi: https://doi.org/10.1002/advs.202408416 has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '45' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Advanced Science publication_identifier: eissn: - 2198-3844 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Protein cage directed assembly of binary nanoparticle superlattices 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 11 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18545' abstract: - lang: eng text: Clinical implementation of therapeutic genome editing relies on efficient in vivo delivery and the safety of CRISPR-Cas tools. Previously, we identified PsCas9 as a Type II-B family enzyme capable of editing mouse liver genome upon adenoviral delivery without detectable off-targets and reduced chromosomal translocations. Yet, its efficacy remains insufficient with non-viral delivery, a common challenge for many Cas9 orthologues. Here, we sought to redesign PsCas9 for in vivo editing using lipid nanoparticles. We solve the PsCas9 ribonucleoprotein structure with cryo-EM and characterize it biochemically, providing a basis for its rational engineering. Screening over numerous guide RNA and protein variants lead us to develop engineered PsCas9 (ePsCas9) with up to 20-fold increased activity across various targets and preserved safety advantages. We apply the same design principles to boost the activity of FnCas9, an enzyme phylogenetically relevant to PsCas9. Remarkably, a single administration of mRNA encoding ePsCas9 and its guide formulated with lipid nanoparticles results in high levels of editing in the Pcsk9 gene in mouse liver, a clinically relevant target for hypercholesterolemia treatment. Collectively, our findings introduce ePsCas9 as a highly efficient, and precise tool for therapeutic genome editing, in addition to the engineering strategy applicable to other Cas9 orthologues. article_number: '9173' article_processing_charge: Yes article_type: original author: - first_name: Dmitrii full_name: Degtev, Dmitrii last_name: Degtev - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Aikaterini full_name: Emmanouilidi, Aikaterini last_name: Emmanouilidi - first_name: Aleksandar full_name: Zdravković, Aleksandar last_name: Zdravković - first_name: Oi Kuan full_name: Choong, Oi Kuan last_name: Choong - first_name: Julia full_name: Liz Touza, Julia last_name: Liz Touza - first_name: Niklas full_name: Selfjord, Niklas last_name: Selfjord - first_name: Isabel full_name: Weisheit, Isabel last_name: Weisheit - first_name: Margherita full_name: Francescatto, Margherita last_name: Francescatto - first_name: Pinar full_name: Akcakaya, Pinar last_name: Akcakaya - first_name: Michelle full_name: Porritt, Michelle last_name: Porritt - first_name: Marcello full_name: Maresca, Marcello last_name: Maresca - first_name: David full_name: Taylor, David last_name: Taylor - first_name: Grzegorz full_name: Sienski, Grzegorz last_name: Sienski citation: ama: Degtev D, Bravo JPK, Emmanouilidi A, et al. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. 2024;15. doi:10.1038/s41467-024-53418-8 apa: Degtev, D., Bravo, J. P. K., Emmanouilidi, A., Zdravković, A., Choong, O. K., Liz Touza, J., … Sienski, G. (2024). Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53418-8 chicago: Degtev, Dmitrii, Jack Peter Kelly Bravo, Aikaterini Emmanouilidi, Aleksandar Zdravković, Oi Kuan Choong, Julia Liz Touza, Niklas Selfjord, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53418-8. ieee: D. Degtev et al., “Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Degtev D, Bravo JPK, Emmanouilidi A, Zdravković A, Choong OK, Liz Touza J, Selfjord N, Weisheit I, Francescatto M, Akcakaya P, Porritt M, Maresca M, Taylor D, Sienski G. 2024. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles. Nature Communications. 15, 9173. mla: Degtev, Dmitrii, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.” Nature Communications, vol. 15, 9173, Springer Nature, 2024, doi:10.1038/s41467-024-53418-8. short: D. Degtev, J.P.K. Bravo, A. Emmanouilidi, A. Zdravković, O.K. Choong, J. Liz Touza, N. Selfjord, I. Weisheit, M. Francescatto, P. Akcakaya, M. Porritt, M. Maresca, D. Taylor, G. Sienski, Nature Communications 15 (2024). date_created: 2024-11-12T10:18:04Z date_published: 2024-11-07T00:00:00Z date_updated: 2024-11-13T08:19:50Z day: '07' ddc: - '572' doi: 10.1038/s41467-024-53418-8 extern: '1' file: - access_level: open_access checksum: dcfadc806f4144d065eb8e2032554782 content_type: application/pdf creator: jbravo date_created: 2024-11-12T10:18:32Z date_updated: 2024-11-12T10:18:32Z file_id: '18546' file_name: s41467-024-53418-8.pdf file_size: 2967001 relation: main_file success: 1 file_date_updated: 2024-11-12T10:18:32Z fulldoi: https://doi.org/10.1038/s41467-024-53418-8 has_accepted_license: '1' intvolume: ' 15' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles 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: 15 year: '2024' ... --- OA_place: publisher _id: '18579' abstract: - lang: eng text: 'Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al. Relevant information can be found in the ''README.txt'' files. ' acknowledged_ssus: - _id: ScienComp - _id: PreCl - _id: M-Shop - _id: Bio - _id: LifeSc acknowledgement: Freyja Lange, Michael Schunn, and Todor Asenov article_processing_charge: No author: - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Anton L full_name: Sumser, Anton L id: 3320A096-F248-11E8-B48F-1D18A9856A87 last_name: Sumser orcid: 0000-0002-4792-1881 - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova orcid: 0000-0003-2012-9947 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Florian full_name: Schmidt, Florian id: A2EF226A-AF19-11E9-924C-0525E6697425 last_name: Schmidt - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 citation: ama: Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:10.15479/AT:ISTA:18579 apa: Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., & Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18579 chicago: Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:18579. ieee: T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024. ista: Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18579. mla: Vega Zuniga, Tomas A., et al. A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:18579. short: T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024). corr_author: '1' date_created: 2024-11-22T13:48:12Z date_published: 2024-12-09T00:00:00Z date_updated: 2026-06-18T18:12:08Z day: '09' ddc: - '570' department: - _id: MaJö doi: 10.15479/AT:ISTA:18579 ec_funded: 1 file: - access_level: open_access checksum: 8b13990ca1a458ae3f3ae54c2e888564 content_type: application/x-zip-compressed creator: symonova date_created: 2024-12-06T13:28:18Z date_updated: 2024-12-09T10:24:25Z file_id: '18625' file_name: electro_physiology_data.zip file_size: 800647957 relation: main_file - access_level: open_access checksum: c5a4d71c5f29c009c3d96a3244532afa content_type: application/x-zip-compressed creator: symonova date_created: 2024-12-09T10:21:10Z date_updated: 2024-12-09T10:21:10Z file_id: '18636' file_name: NN_vLGN_Ca_data.zip file_size: 828410832 relation: main_file success: 1 - access_level: open_access checksum: 63651df0186196969553dc48b467f6ab content_type: text/plain creator: symonova date_created: 2024-12-09T12:54:55Z date_updated: 2024-12-09T12:54:55Z file_id: '18637' file_name: readme.txt file_size: 505 relation: main_file success: 1 file_date_updated: 2024-12-09T12:54:55Z fulldoi: https://doi.org/10.15479/AT:ISTA:18579 has_accepted_license: '1' month: '12' oa: 1 oa_version: Published Version project: - _id: 264FEA02-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1098-2017 name: Connecting sensory with motor processing in the superior colliculus - _id: 266D407A-B435-11E9-9278-68D0E5697425 grant_number: LT000256 name: Neuronal networks of salience and spatial detection in the murine superior colliculus - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention - _id: bdaf81a8-d553-11ed-ba76-c95961984540 grant_number: '101086580' name: 'Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses' publisher: Institute of Science and Technology Austria related_material: record: - id: '19076' relation: used_in_publication status: public status: public title: A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18645' abstract: - lang: eng text: Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA ‘unwrapping’. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming. acknowledgement: 'We are very grateful to K. Abe, L. G. Hernandez, C. Kobayashi, K. Straßer and M. Zaczek for their contributions and technical support. We thank N. Thomä for advice on SeEN-seq. We are grateful to A. Musacchio for insightful discussions. We thank J.-M. Peters for critical reading of the manuscript and all members of K.T.’s laboratory for discussions. We thank T. Schäfer at the cryo-EM facility for assistance in cryo-EM data collection, and R. H. Kim for sequencing at the NGS facility, MPIB. K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich. Funding: European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.). European Research Council grant ERC-StG-804098 ReplisomeBypass (K.D.). Max Planck Society (K.T., K.D.).' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Wataru full_name: Kobayashi, Wataru last_name: Kobayashi - first_name: Anna H. full_name: Sappler, Anna H. last_name: Sappler - first_name: Daniel full_name: Bollschweiler, Daniel last_name: Bollschweiler - first_name: Maximilian full_name: Kümmecke, Maximilian last_name: Kümmecke - first_name: Jérôme full_name: Basquin, Jérôme last_name: Basquin - first_name: Eda Nur full_name: Arslantas, Eda Nur id: 36978b4e-2966-11ef-a72f-b3740ef1cd11 last_name: Arslantas - first_name: Siwat full_name: Ruangroengkulrith, Siwat last_name: Ruangroengkulrith - first_name: Renate full_name: Hornberger, Renate last_name: Hornberger - first_name: Karl full_name: Duderstadt, Karl last_name: Duderstadt - first_name: Kikuë full_name: Tachibana, Kikuë last_name: Tachibana citation: ama: Kobayashi W, Sappler AH, Bollschweiler D, et al. Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition. Nature Structural & Molecular Biology. 2024;31:757-766. doi:10.1038/s41594-024-01239-0 apa: Kobayashi, W., Sappler, A. H., Bollschweiler, D., Kümmecke, M., Basquin, J., Arslantas, E. N., … Tachibana, K. (2024). Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01239-0 chicago: Kobayashi, Wataru, Anna H. Sappler, Daniel Bollschweiler, Maximilian Kümmecke, Jérôme Basquin, Eda Nur Arslantas, Siwat Ruangroengkulrith, Renate Hornberger, Karl Duderstadt, and Kikuë Tachibana. “Nucleosome-Bound NR5A2 Structure Reveals Pioneer Factor Mechanism by DNA Minor Groove Anchor Competition.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-024-01239-0. ieee: W. Kobayashi et al., “Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition,” Nature Structural & Molecular Biology, vol. 31. Springer Nature, pp. 757–766, 2024. ista: Kobayashi W, Sappler AH, Bollschweiler D, Kümmecke M, Basquin J, Arslantas EN, Ruangroengkulrith S, Hornberger R, Duderstadt K, Tachibana K. 2024. Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition. Nature Structural & Molecular Biology. 31, 757–766. mla: Kobayashi, Wataru, et al. “Nucleosome-Bound NR5A2 Structure Reveals Pioneer Factor Mechanism by DNA Minor Groove Anchor Competition.” Nature Structural & Molecular Biology, vol. 31, Springer Nature, 2024, pp. 757–66, doi:10.1038/s41594-024-01239-0. short: W. Kobayashi, A.H. Sappler, D. Bollschweiler, M. Kümmecke, J. Basquin, E.N. Arslantas, S. Ruangroengkulrith, R. Hornberger, K. Duderstadt, K. Tachibana, Nature Structural & Molecular Biology 31 (2024) 757–766. date_created: 2024-12-11T09:10:54Z date_published: 2024-05-01T00:00:00Z date_updated: 2024-12-11T10:56:35Z day: '01' doi: 10.1038/s41594-024-01239-0 extern: '1' fulldoi: https://doi.org/10.1038/s41594-024-01239-0 intvolume: ' 31' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41594-024-01239-0 month: '05' oa: 1 oa_version: Published Version page: 757-766 publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2024' ... --- OA_place: repository OA_type: green _id: '18756' abstract: - lang: eng text: "The evasive LWE assumption, proposed by Wee [Eurocrypt’22 Wee] for constructing a lattice-based optimal broadcast encryption, has shown to be a powerful assumption, adopted by subsequent works to construct advanced primitives ranging from ABE variants to obfuscation for null circuits. However, a closer look reveals significant differences among the precise assumption statements involved in different works, leading to the fundamental question of how these assumptions compare to each other. In this work, we initiate a more systematic study on evasive LWE assumptions:\r\n(i) Based on the standard LWE assumption, we construct simple counterexamples against three private-coin evasive LWE variants, used in [Crypto’22 Tsabary, Asiacrypt’22 VWW, Crypto’23 ARYY] respectively, showing that these assumptions are unlikely to hold.\r\n\r\n(ii) Based on existing evasive LWE variants and our counterexamples, we propose and define three classes of plausible evasive LWE assumptions, suitably capturing all existing variants for which we are not aware of non-obfuscation-based counterexamples.\r\n\r\n(iii) We show that under our assumption formulations, the security proofs of [Asiacrypt’22 VWW] and [Crypto’23 ARYY] can be recovered, and we reason why the security proof of [Crypto’22 Tsabary] is also plausibly repairable using an appropriate evasive LWE assumption." acknowledgement: The authors thank the anonymous reviewers for insightful comments which very much improved this work, in particular, sharing with us the counterexamples against a prior version of Hiding Evasive LWE, and against public-coin Evasive LWE when the sampler inputs B. Chris Brzuska and Ivy K. Y. Woo are supported by Research Council of Finland grant 358950. We thank Russell W. F. Lai and Hoeteck Wee for helpful discussions. alternative_title: - LNCS article_processing_charge: No author: - first_name: Chris full_name: Brzuska, Chris last_name: Brzuska - first_name: Akin full_name: Ünal, Akin id: f6b56fb6-dc63-11ee-9dbf-f6780863a85a last_name: Ünal orcid: 0000-0002-8929-0221 - first_name: Ivy K.Y. full_name: Woo, Ivy K.Y. last_name: Woo citation: ama: 'Brzuska C, Ünal A, Woo IKY. Evasive LWE assumptions: Definitions, classes, and counterexamples. In: 30th International Conference on the Theory and Application of Cryptology and Information Security. Vol 15487. Springer Nature; 2024:418-449. doi:10.1007/978-981-96-0894-2_14' apa: 'Brzuska, C., Ünal, A., & Woo, I. K. Y. (2024). Evasive LWE assumptions: Definitions, classes, and counterexamples. In 30th International Conference on the Theory and Application of Cryptology and Information Security (Vol. 15487, pp. 418–449). Kolkata, India: Springer Nature. https://doi.org/10.1007/978-981-96-0894-2_14' chicago: 'Brzuska, Chris, Akin Ünal, and Ivy K.Y. Woo. “Evasive LWE Assumptions: Definitions, Classes, and Counterexamples.” In 30th International Conference on the Theory and Application of Cryptology and Information Security, 15487:418–49. Springer Nature, 2024. https://doi.org/10.1007/978-981-96-0894-2_14.' ieee: 'C. Brzuska, A. Ünal, and I. K. Y. Woo, “Evasive LWE assumptions: Definitions, classes, and counterexamples,” in 30th International Conference on the Theory and Application of Cryptology and Information Security, Kolkata, India, 2024, vol. 15487, pp. 418–449.' ista: 'Brzuska C, Ünal A, Woo IKY. 2024. Evasive LWE assumptions: Definitions, classes, and counterexamples. 30th International Conference on the Theory and Application of Cryptology and Information Security. ASIACRYPT: Conference on the Theory and Application of Cryptology and Information Security, LNCS, vol. 15487, 418–449.' mla: 'Brzuska, Chris, et al. “Evasive LWE Assumptions: Definitions, Classes, and Counterexamples.” 30th International Conference on the Theory and Application of Cryptology and Information Security, vol. 15487, Springer Nature, 2024, pp. 418–49, doi:10.1007/978-981-96-0894-2_14.' short: C. Brzuska, A. Ünal, I.K.Y. Woo, in:, 30th International Conference on the Theory and Application of Cryptology and Information Security, Springer Nature, 2024, pp. 418–449. conference: end_date: 2024-12-13 location: Kolkata, India name: 'ASIACRYPT: Conference on the Theory and Application of Cryptology and Information Security' start_date: 2024-12-09 date_created: 2025-01-05T23:01:56Z date_published: 2024-12-13T00:00:00Z date_updated: 2025-09-09T12:00:51Z day: '13' department: - _id: KrPi doi: 10.1007/978-981-96-0894-2_14 external_id: isi: - '001443890800014' fulldoi: https://doi.org/10.1007/978-981-96-0894-2_14 intvolume: ' 15487' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2024/2000 month: '12' oa: 1 oa_version: Preprint page: 418-449 publication: 30th International Conference on the Theory and Application of Cryptology and Information Security publication_identifier: eissn: - 1611-3349 isbn: - '9789819608935' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Evasive LWE assumptions: Definitions, classes, and counterexamples' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15487 year: '2024' ... --- OA_type: closed access _id: '18867' abstract: - lang: eng text: 'In an accreting X-ray pulsar, a neutron star accretes matter from a companion star through an accretion disk. The magnetic field of the rotating neutron star disrupts the inner edge of the disk, funnelling the gas to flow onto the poles on its surface. Hercules X-1 is a prototypical persistent X-ray pulsar about 7 kpc from Earth. Its emission varies on three distinct timescales: the neutron star rotates every 1.2 s, it is eclipsed by its companion each 1.7 d, and the system exhibits a superorbital period of 35 d, which has remained stable since its discovery. Several lines of evidence point to the source of this variation as the precession of the accretion disk or that of the neutron star. Despite the many hints over the past 50 yr, the precession of the neutron star itself has yet not been confirmed or refuted. X-ray polarization measurements (probing the spin geometry of Her X-1) with the Imaging X-ray Polarimetry Explorer suggest that free precession of the neutron star crust sets the 35 d period; this has the important implication that its crust is somewhat asymmetric by a few parts per ten million.' article_processing_charge: No article_type: original author: - first_name: Jeremy full_name: Heyl, Jeremy last_name: Heyl - first_name: Victor full_name: Doroshenko, Victor last_name: Doroshenko - first_name: Denis full_name: González-Caniulef, Denis last_name: González-Caniulef - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Juri full_name: Poutanen, Juri last_name: Poutanen - first_name: Alexander full_name: Mushtukov, Alexander last_name: Mushtukov - first_name: Sergey S. full_name: Tsygankov, Sergey S. last_name: Tsygankov - first_name: Demet full_name: Kirmizibayrak, Demet last_name: Kirmizibayrak - first_name: Matteo full_name: Bachetti, Matteo last_name: Bachetti - first_name: George G. full_name: Pavlov, George G. last_name: Pavlov - first_name: Sofia V. full_name: Forsblom, Sofia V. last_name: Forsblom - first_name: Christian full_name: Malacaria, Christian last_name: Malacaria - first_name: Valery F. full_name: Suleimanov, Valery F. last_name: Suleimanov - first_name: Iván full_name: Agudo, Iván last_name: Agudo - first_name: Lucio Angelo full_name: Antonelli, Lucio Angelo last_name: Antonelli - first_name: Luca full_name: Baldini, Luca last_name: Baldini - first_name: Wayne H. full_name: Baumgartner, Wayne H. last_name: Baumgartner - first_name: Ronaldo full_name: Bellazzini, Ronaldo last_name: Bellazzini - first_name: Stefano full_name: Bianchi, Stefano last_name: Bianchi - first_name: Stephen D. full_name: Bongiorno, Stephen D. last_name: Bongiorno - first_name: Raffaella full_name: Bonino, Raffaella last_name: Bonino - first_name: Alessandro full_name: Brez, Alessandro last_name: Brez - first_name: Niccolò full_name: Bucciantini, Niccolò last_name: Bucciantini - first_name: Fiamma full_name: Capitanio, Fiamma last_name: Capitanio - first_name: Simone full_name: Castellano, Simone last_name: Castellano - first_name: Elisabetta full_name: Cavazzuti, Elisabetta last_name: Cavazzuti - first_name: Chien-Ting full_name: Chen, Chien-Ting last_name: Chen - first_name: Stefano full_name: Ciprini, Stefano last_name: Ciprini - first_name: Enrico full_name: Costa, Enrico last_name: Costa - first_name: Alessandra full_name: De Rosa, Alessandra last_name: De Rosa - first_name: Ettore full_name: Del Monte, Ettore last_name: Del Monte - first_name: Laura full_name: Di Gesu, Laura last_name: Di Gesu - first_name: Niccolò full_name: Di Lalla, Niccolò last_name: Di Lalla - first_name: Alessandro full_name: Di Marco, Alessandro last_name: Di Marco - first_name: Immacolata full_name: Donnarumma, Immacolata last_name: Donnarumma - first_name: Michal full_name: Dovčiak, Michal last_name: Dovčiak - first_name: Steven R. full_name: Ehlert, Steven R. last_name: Ehlert - first_name: Teruaki full_name: Enoto, Teruaki last_name: Enoto - first_name: Yuri full_name: Evangelista, Yuri last_name: Evangelista - first_name: Sergio full_name: Fabiani, Sergio last_name: Fabiani - first_name: Riccardo full_name: Ferrazzoli, Riccardo last_name: Ferrazzoli - first_name: Javier A. full_name: Garcia, Javier A. last_name: Garcia - first_name: Shuichi full_name: Gunji, Shuichi last_name: Gunji - first_name: Kiyoshi full_name: Hayashida, Kiyoshi last_name: Hayashida - first_name: Wataru full_name: Iwakiri, Wataru last_name: Iwakiri - first_name: Svetlana G. full_name: Jorstad, Svetlana G. last_name: Jorstad - first_name: Philip full_name: Kaaret, Philip last_name: Kaaret - first_name: Vladimir full_name: Karas, Vladimir last_name: Karas - first_name: Fabian full_name: Kislat, Fabian last_name: Kislat - first_name: Takao full_name: Kitaguchi, Takao last_name: Kitaguchi - first_name: Jeffery J. full_name: Kolodziejczak, Jeffery J. last_name: Kolodziejczak - first_name: Henric full_name: Krawczynski, Henric last_name: Krawczynski - first_name: Fabio full_name: La Monaca, Fabio last_name: La Monaca - first_name: Luca full_name: Latronico, Luca last_name: Latronico - first_name: Ioannis full_name: Liodakis, Ioannis last_name: Liodakis - first_name: Simone full_name: Maldera, Simone last_name: Maldera - first_name: Alberto full_name: Manfreda, Alberto last_name: Manfreda - first_name: Frédéric full_name: Marin, Frédéric last_name: Marin - first_name: Andrea full_name: Marinucci, Andrea last_name: Marinucci - first_name: Alan P. full_name: Marscher, Alan P. last_name: Marscher - first_name: Herman L. full_name: Marshall, Herman L. last_name: Marshall - first_name: Francesco full_name: Massaro, Francesco last_name: Massaro - first_name: Giorgio full_name: Matt, Giorgio last_name: Matt - first_name: Ikuyuki full_name: Mitsuishi, Ikuyuki last_name: Mitsuishi - first_name: Tsunefumi full_name: Mizuno, Tsunefumi last_name: Mizuno - first_name: Fabio full_name: Muleri, Fabio last_name: Muleri - first_name: Michela full_name: Negro, Michela last_name: Negro - first_name: C.-Y. full_name: Ng, C.-Y. last_name: Ng - first_name: Stephen L. full_name: O’Dell, Stephen L. last_name: O’Dell - first_name: Nicola full_name: Omodei, Nicola last_name: Omodei - first_name: Chiara full_name: Oppedisano, Chiara last_name: Oppedisano - first_name: Alessandro full_name: Papitto, Alessandro last_name: Papitto - first_name: Abel Lawrence full_name: Peirson, Abel Lawrence last_name: Peirson - first_name: Matteo full_name: Perri, Matteo last_name: Perri - first_name: Melissa full_name: Pesce-Rollins, Melissa last_name: Pesce-Rollins - first_name: Pierre-Olivier full_name: Petrucci, Pierre-Olivier last_name: Petrucci - first_name: Maura full_name: Pilia, Maura last_name: Pilia - first_name: Andrea full_name: Possenti, Andrea last_name: Possenti - first_name: Simonetta full_name: Puccetti, Simonetta last_name: Puccetti - first_name: Brian D. full_name: Ramsey, Brian D. last_name: Ramsey - first_name: John full_name: Rankin, John last_name: Rankin - first_name: Ajay full_name: Ratheesh, Ajay last_name: Ratheesh - first_name: Oliver J. full_name: Roberts, Oliver J. last_name: Roberts - first_name: Roger W. full_name: Romani, Roger W. last_name: Romani - first_name: Carmelo full_name: Sgrò, Carmelo last_name: Sgrò - first_name: Patrick full_name: Slane, Patrick last_name: Slane - first_name: Paolo full_name: Soffitta, Paolo last_name: Soffitta - first_name: Gloria full_name: Spandre, Gloria last_name: Spandre - first_name: Douglas A. full_name: Swartz, Douglas A. last_name: Swartz - first_name: Toru full_name: Tamagawa, Toru last_name: Tamagawa - first_name: Fabrizio full_name: Tavecchio, Fabrizio last_name: Tavecchio - first_name: Roberto full_name: Taverna, Roberto last_name: Taverna - first_name: Yuzuru full_name: Tawara, Yuzuru last_name: Tawara - first_name: Allyn F. full_name: Tennant, Allyn F. last_name: Tennant - first_name: Nicholas E. full_name: Thomas, Nicholas E. last_name: Thomas - first_name: Francesco full_name: Tombesi, Francesco last_name: Tombesi - first_name: Alessio full_name: Trois, Alessio last_name: Trois - first_name: Roberto full_name: Turolla, Roberto last_name: Turolla - first_name: Jacco full_name: Vink, Jacco last_name: Vink - first_name: Martin C. full_name: Weisskopf, Martin C. last_name: Weisskopf - first_name: Kinwah full_name: Wu, Kinwah last_name: Wu - first_name: Fei full_name: Xie, Fei last_name: Xie - first_name: Silvia full_name: Zane, Silvia last_name: Zane citation: ama: Heyl J, Doroshenko V, González-Caniulef D, et al. Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization. Nature Astronomy. 2024;8:1047-1053. doi:10.1038/s41550-024-02295-8 apa: Heyl, J., Doroshenko, V., González-Caniulef, D., Caiazzo, I., Poutanen, J., Mushtukov, A., … Zane, S. (2024). Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-024-02295-8 chicago: Heyl, Jeremy, Victor Doroshenko, Denis González-Caniulef, Ilaria Caiazzo, Juri Poutanen, Alexander Mushtukov, Sergey S. Tsygankov, et al. “Complex Rotational Dynamics of the Neutron Star in Hercules X-1 Revealed by X-Ray Polarization.” Nature Astronomy. Springer Nature, 2024. https://doi.org/10.1038/s41550-024-02295-8. ieee: J. Heyl et al., “Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization,” Nature Astronomy, vol. 8. Springer Nature, pp. 1047–1053, 2024. ista: Heyl J et al. 2024. Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization. Nature Astronomy. 8, 1047–1053. mla: Heyl, Jeremy, et al. “Complex Rotational Dynamics of the Neutron Star in Hercules X-1 Revealed by X-Ray Polarization.” Nature Astronomy, vol. 8, Springer Nature, 2024, pp. 1047–53, doi:10.1038/s41550-024-02295-8. short: J. Heyl, V. Doroshenko, D. González-Caniulef, I. Caiazzo, J. Poutanen, A. Mushtukov, S.S. Tsygankov, D. Kirmizibayrak, M. Bachetti, G.G. Pavlov, S.V. Forsblom, C. Malacaria, V.F. Suleimanov, I. Agudo, L.A. Antonelli, L. Baldini, W.H. Baumgartner, R. Bellazzini, S. Bianchi, S.D. Bongiorno, R. Bonino, A. Brez, N. Bucciantini, F. Capitanio, S. Castellano, E. Cavazzuti, C.-T. Chen, S. Ciprini, E. Costa, A. De Rosa, E. Del Monte, L. Di Gesu, N. Di Lalla, A. Di Marco, I. Donnarumma, M. Dovčiak, S.R. Ehlert, T. Enoto, Y. Evangelista, S. Fabiani, R. Ferrazzoli, J.A. Garcia, S. Gunji, K. Hayashida, W. Iwakiri, S.G. Jorstad, P. Kaaret, V. Karas, F. Kislat, T. Kitaguchi, J.J. Kolodziejczak, H. Krawczynski, F. La Monaca, L. Latronico, I. Liodakis, S. Maldera, A. Manfreda, F. Marin, A. Marinucci, A.P. Marscher, H.L. Marshall, F. Massaro, G. Matt, I. Mitsuishi, T. Mizuno, F. Muleri, M. Negro, C.-Y. Ng, S.L. O’Dell, N. Omodei, C. Oppedisano, A. Papitto, A.L. Peirson, M. Perri, M. Pesce-Rollins, P.-O. Petrucci, M. Pilia, A. Possenti, S. Puccetti, B.D. Ramsey, J. Rankin, A. Ratheesh, O.J. Roberts, R.W. Romani, C. Sgrò, P. Slane, P. Soffitta, G. Spandre, D.A. Swartz, T. Tamagawa, F. Tavecchio, R. Taverna, Y. Tawara, A.F. Tennant, N.E. Thomas, F. Tombesi, A. Trois, R. Turolla, J. Vink, M.C. Weisskopf, K. Wu, F. Xie, S. Zane, Nature Astronomy 8 (2024) 1047–1053. date_created: 2025-01-21T15:35:17Z date_published: 2024-08-01T00:00:00Z date_updated: 2025-01-27T10:52:16Z day: '01' doi: 10.1038/s41550-024-02295-8 extern: '1' fulldoi: https://doi.org/10.1038/s41550-024-02295-8 intvolume: ' 8' language: - iso: eng month: '08' oa_version: None page: 1047-1053 publication: Nature Astronomy publication_identifier: issn: - 2397-3366 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18868' abstract: - lang: eng text: We develop two new highly efficient estimators to measure the polarization (Stokes parameters) in experiments that constrain the position angle of individual photons such as scattering and gas-pixel-detector polarimeters, and analyse in detail a previously proposed estimator. All three of these estimators are at least fifty percent more efficient on typical datasets than the standard estimator used in the field. We present analytic estimates of the variance of these estimators and numerical experiments to verify these estimates. Two of the three estimators can be calculated quickly and directly through summations over the measurements of individual photons. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jeremy full_name: Heyl, Jeremy last_name: Heyl - first_name: Denis full_name: González-Caniulef, Denis last_name: González-Caniulef - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 citation: ama: Heyl J, González-Caniulef D, Caiazzo I. Optimal summary statistics for X-ray polarization. The Open Journal of Astrophysics. 2024;7. doi:10.33232/001c.117476 apa: Heyl, J., González-Caniulef, D., & Caiazzo, I. (2024). Optimal summary statistics for X-ray polarization. The Open Journal of Astrophysics. Maynooth Academic Publishing. https://doi.org/10.33232/001c.117476 chicago: Heyl, Jeremy, Denis González-Caniulef, and Ilaria Caiazzo. “Optimal Summary Statistics for X-Ray Polarization.” The Open Journal of Astrophysics. Maynooth Academic Publishing, 2024. https://doi.org/10.33232/001c.117476. ieee: J. Heyl, D. González-Caniulef, and I. Caiazzo, “Optimal summary statistics for X-ray polarization,” The Open Journal of Astrophysics, vol. 7. Maynooth Academic Publishing, 2024. ista: Heyl J, González-Caniulef D, Caiazzo I. 2024. Optimal summary statistics for X-ray polarization. The Open Journal of Astrophysics. 7. mla: Heyl, Jeremy, et al. “Optimal Summary Statistics for X-Ray Polarization.” The Open Journal of Astrophysics, vol. 7, Maynooth Academic Publishing, 2024, doi:10.33232/001c.117476. short: J. Heyl, D. González-Caniulef, I. Caiazzo, The Open Journal of Astrophysics 7 (2024). date_created: 2025-01-21T15:54:16Z date_published: 2024-05-01T00:00:00Z date_updated: 2025-01-27T10:48:19Z day: '01' doi: 10.33232/001c.117476 extern: '1' external_id: arxiv: - '2311.07805' fulldoi: https://doi.org/10.33232/001c.117476 intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.33232/001c.117476 month: '05' oa: 1 oa_version: Published Version publication: The Open Journal of Astrophysics publication_identifier: issn: - 2565-6120 publication_status: published publisher: Maynooth Academic Publishing quality_controlled: '1' scopus_import: '1' status: public title: Optimal summary statistics for X-ray polarization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18998' abstract: - lang: eng text: Word embeddings represent language vocabularies as clouds of d-dimensional points. We investigate how information is conveyed by the general shape of these clouds, instead of representing the semantic meaning of each token. Specifically, we use the notion of persistent homology from topological data analysis (TDA) to measure the distances between language pairs from the shape of their unlabeled embeddings. These distances quantify the degree of non-isometry of the embeddings. To distinguish whether these differences are random training errors or capture real information about the languages, we use the computed distance matrices to construct language phylogenetic trees over 81 Indo-European languages. Careful evaluation shows that our reconstructed trees exhibit strong and statistically-significant similarities to the reference. article_processing_charge: No arxiv: 1 author: - first_name: Ondrej full_name: Draganov, Ondrej id: 2B23F01E-F248-11E8-B48F-1D18A9856A87 last_name: Draganov orcid: 0000-0003-0464-3823 - first_name: Steven full_name: Skiena, Steven last_name: Skiena citation: ama: 'Draganov O, Skiena S. The shape of word embeddings: Quantifying non-isometry with topological data analysis. In: Findings of the Association for Computational Linguistics: EMNLP 2024. Association for Computational Linguistics; 2024:12080-12099. doi:10.18653/v1/2024.findings-emnlp.705' apa: 'Draganov, O., & Skiena, S. (2024). The shape of word embeddings: Quantifying non-isometry with topological data analysis. In Findings of the Association for Computational Linguistics: EMNLP 2024 (pp. 12080–12099). Miami, FL, United States: Association for Computational Linguistics. https://doi.org/10.18653/v1/2024.findings-emnlp.705' chicago: 'Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” In Findings of the Association for Computational Linguistics: EMNLP 2024, 12080–99. Association for Computational Linguistics, 2024. https://doi.org/10.18653/v1/2024.findings-emnlp.705.' ieee: 'O. Draganov and S. Skiena, “The shape of word embeddings: Quantifying non-isometry with topological data analysis,” in Findings of the Association for Computational Linguistics: EMNLP 2024, Miami, FL, United States, 2024, pp. 12080–12099.' ista: 'Draganov O, Skiena S. 2024. The shape of word embeddings: Quantifying non-isometry with topological data analysis. Findings of the Association for Computational Linguistics: EMNLP 2024. EMNLP: Conference on Empirical Methods in Natural Language Processing, 12080–12099.' mla: 'Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–99, doi:10.18653/v1/2024.findings-emnlp.705.' short: 'O. Draganov, S. Skiena, in:, Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–12099.' conference: end_date: 2024-11-16 location: Miami, FL, United States name: 'EMNLP: Conference on Empirical Methods in Natural Language Processing' start_date: 2024-11-12 corr_author: '1' date_created: 2025-02-04T16:19:28Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-02-10T08:21:37Z day: '01' ddc: - '500' department: - _id: GradSch - _id: HeEd doi: 10.18653/v1/2024.findings-emnlp.705 external_id: arxiv: - '2404.00500' file: - access_level: open_access checksum: f4416a5962194f0181ab0dc7f9ef93c0 content_type: application/pdf creator: dernst date_created: 2025-02-10T08:20:34Z date_updated: 2025-02-10T08:20:34Z file_id: '19016' file_name: 2024_EMNLP_Draganov.pdf file_size: 1312638 relation: main_file success: 1 file_date_updated: 2025-02-10T08:20:34Z fulldoi: https://doi.org/10.18653/v1/2024.findings-emnlp.705 has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 12080-12099 publication: 'Findings of the Association for Computational Linguistics: EMNLP 2024' publication_status: published publisher: Association for Computational Linguistics quality_controlled: '1' scopus_import: '1' status: public title: 'The shape of word embeddings: Quantifying non-isometry with topological data analysis' 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ...