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PhasAGE Training School 1 - Linear motifs identification and prediction - PRACTICAL
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
<p>This dataset includes 20 supplementary data files for manuscript <em>Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins </em>by Jakub W. Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virginie Coustou, Natalia Szulc, Monika Szefczyk, Marta Kopaczyńska, Sven J. Saupe, and Witold Dyrka (under revision). </p> <ul> <li>SF2. Profile HMMs of NLR effector domains. The file includes previously unpublished models.</li> <li>SF3. Multiple sequence alignments of N-termini clusters. </li> <li>SF4. Tabularized results of N-termini annotation.</li> <li>SF5. Structure prediction of HeLo-/Goodbye-/MLKL-like domains. Full AlphaFold2/ColabFold outputs.</li> <li>SF6. Structure prediction of previously unannotated domains. Full AlphaFold2/ColabFold outputs.</li> <li>SF7. PCFGs for BASS. The file includes previously unpublished grammars and a sample scanning configuration.</li> <li>SF8. Candidate short NLR N-termini with ASMs. The FASTA file includes sequences from clusters with high content of ASM-like sequences, according to the BASS PCFGs (SF7).</li> <li>SF9. Profile HMMs of ASMs found in short NLR N-termini.</li> <li>SF10. Profile HMM of HeLo-related HRAMs.</li> <li>SF11. Genomic neighbors of candidate short N-termini NLRs with ASMs The list includes accessions of proteins encoded by genes within the neighborhood of 20kbp of genes encoding the query proteins (SF8).</li> <li>SF12. Short C-termini of 200–400 aa long proteins genomically neighboring candidate short NLR N-termini with ASMs. The FASTA file concerns target proteins listed in SF11.</li> <li>SF13. Pairwise hits of the same ASMs in N-termini of NLRs and C-termini of genomically neighboring proteins. The table is based on SF8–9 and SF11–12. </li> <li>SF14. Lists of HMMER domain hits of effector domain profiles. The lists were obtained through iterative searches in NCBI “nr” starting from Pfam profiles of known NLR effector domains.</li> <li>SF15. Short C-termini of effector proteins. The FASTA file concerns target proteins listed in SF14.</li> <li>SF16. Short N-termini of Pfam NACHT and NB-ARC proteins. The FASTA file concerns proteins from NCBI “nr” associated with the two families in the Pfam database.</li> <li>SF17. Profile HMMs of ASMs found both in effector C-termini and NLR N-termini of genomically neighboring proteins.</li> <li>SF18. Genomic neighbors of candidate short N-termini Pfam NACHT and NB-ARC proteins. The list includes accessions of proteins encoded by genes within the neighborhood of 20kbp of genes encoding the query proteins (SF16).</li> <li>SF19. Pairwise hits of the same ASMs in N-termini of NACHT/NB-ARC NLRs and C-termini of genomically neighboring effector proteins. The table is based on SF15–18. </li> <li>SF20. Pairwise hits of the same ASMs in N-termini of NLRs and C-termini of genomically co-occurring effector proteins. The table is based on SF8–9 and SF15. </li> <li>SF21. BaMLKL homologs identified with hmmsearch in Basidiomycota. A FASTA file.</li> </ul>
Research data supporting: "Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"
<p>This repository contains the set of data shown in the paper <strong>"Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"</strong>, published on The Journal of Physical Chemistry B (DOI:10.1021/acs.jpcb.2c08726).</p>
Supplementary Videos: The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition
<p>Supplementary Movies associated with the following work: "The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition", available as a preprint on chemRxiv: https://chemrxiv.org/articles/preprint/The_N-Terminal_Helix-Turn-Helix_Motif_of_Transcription_Factors_MarA_and_Rob_Drives_DNA_Recognition/12195372 </p>
FIG. 14. — A in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 14. — A, Cryptochorda (s.str.) altavesna n. sp. Lutétiende Parnes (Oise). MNHN.F.A57647 (coll. Brongniart), H.: 45,5 mm; B -D, étiquettes originales de la collection Brongniart; E, Cryptochorda (s.str.) stromboides (Hermann, 1781), Lutétien de Thiverval-Grignon (Yvelines). MNHN.F.A57591 (coll. Brongniart), H.: 49,4 mm; F, Cryptochorda (s.str.) altavesna n. sp. Figure originalede Buccinum stromboides « variété a » Deshayes, 1835. D'après Deshayes (1853).
FIG. 13. — A-G in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 13. — A-G, Cryptochorda (s.str.) cosediensis n. sp. A-D, Lutétiende Fresville (Manche); E-G, Lutétiende Hautteville-Bocage (Manche). A, Holotype MNHN.F.B65189 (coll. de Morgan), H.: 49,8 mm; B, Paratype MNHN.F.A71456 (coll. de Morgan), H.: 35,5 mm; C, Paratype MNHN.F.A71457 (coll. de Morgan), H.: 44,3 mm; D, Paratype MNHN.F.A05108 (coll. Le Marchand), H.: 39,2 mm; E, spécimen juvénile, MNHN.F.A71458, H.: 19,1 mm; F, spécimen juvénile, MNHN.F.A71459, H.: 30,7 mm; G, MNHN.F.A71458, protoconque. Échelle: G, 2 mm.
FIG. 12 in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 12. — Motifs colorés résiduels révélés sous lumière UV sur des spécimens juvéniles et adultes. A-D, Cryptochorda (s.str.) pyrenaicensis Cossmann, 1923. Cuisien (Yprésien) dela Tuilerie, Gan (Pyrénées-Atlantiques). E-J. Cryptochorda (s.str.) neptis n. sp. E-G, Cuisien (Yprésien) de Mons-en-Laonnois (Aisne); H-J, Cuisien (Yprésien) de Saint-Gobain (Aisne). K-M, Cryptochorda (s.str.) cosediensis n. sp. K, M, Lutétiende Fresville (Manche); L, Lutétiende Hautteville- Bocage (Manche). A, MNHN.F.A71481 (coll. O'Gorman), H.: 24,9 mm; B, MNHN.F.J10882 (coll. O'Gorman), H.: 25,7 mm; C, MNHN.F.A57359 (coll. Pacaud), H.: 34,2 mm; D, MNHN.F.J14638 (coll. Cossmann), H.: 37,2 mm; E, MNHN.F.A71452 (coll. Lhomme), H.: 37,3 mm; F, MNHN.F.A71453 (coll. Lhomme), H.: 40,7 mm; G, MNHN.F.A71454 (coll. Lhomme), H.: 26,4 mm; H, Paratype MNHN.F.A71450 (coll. Romanek), H.: 29,0 mm; I, Paratype MNHN.F.A71451 (coll. Romanek), H.: 34,9 mm; J, MNHN.F.A71455 (coll. Pacaud), H.: 30,0 mm; K, MNHN.F.A71458, H.: 19,1 mm; L, MNHN.F.A71460, H.: 42,5 mm; M, Paratype MNHN.F.A71461 (coll. de Morgan), H.: 32,9 mm.
FIG. 11. — A-J in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 11. — A-J, Cryptochorda (s.str.) neptis n. sp. A-H, Cuisien (Yprésien) de Saint-Gobain (Aisne); I-J, Panisélien (Yprésien) d'Egem (Belgique). A, Holotype MNHN.F.A71442 (coll. Pacaud), H.: 37,1 mm; B, Paratype MNHN.F.A71443 (coll. Pacaud), H.: 37,5 mm; C, Paratype MNHN.F.A71444 (coll. Pacaud), H.: 34,0 mm; D, Paratype MNHN.F.A71445 (coll. Romanek), H.: 30,1 mm; E, Paratype MNHN.F.A71446 (coll. Pacaud), H.: 43,3 mm; F, spécimen juvénile, Paratype MNHN.F.A71447 (coll. Romanek), H.: 18,7 mm; G, spécimen juvénile, Paratype MNHN.F.A71448 (coll. Romanek), H.: 29,2 mm; H, Paratype MNHN.F.A71449 (coll. Pacaud), protoconque; I, MNHN.F.A71462 (coll. Merle), H.: 33,6 mm; J, MNHN.F.A71463 (coll. Merle), H.: 35,4 mm. Échelle: H, 2 mm.
FIG. 6. — A-L in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 6. — A-L, Cryptochorda (s.str.) stromboides (Hermann, 1781). A, Néotype MNHN.F.A57573 (coll. de Roissy), Lutétiende Courtagnon (Marne), H.: 55,7 mm; B, MNHN.FA71408 (coll. Pacaud), Lutétiende Damery (Marne), H.: 46,7 mm; C, MNHN.F.A71409 (coll. Staadt), Lutétiende Damery (Marne), H.: 51,6 mm; D, MNHN.F.A71410 (coll. d'Orbigny), Lutétiende Thiverval-Grignon (Yvelines), H.: 61,2 mm; E, MNHN.F.A71411 (coll. Pacaud), Lutétiende Damery (Marne), H.: 48,0 mm; F, MNHN.F.A71412 (coll. Pacaud), Lutétiende Damery (Marne), H.: 55,5 mm; G, MNHN.F.A71413 (coll. Faullummel), Auversien (Bartonien) de Mécringes (Marne), H.: 48,0 mm; H, spécimen juvénile, MNHN.F.A71414 (coll. Staadt), Lutétien de Damery (Marne), H.: 27,7 mm; I, spécimen juvénile, MNHN.F.A71415 (coll. Staadt), Lutétiende Damery (Marne), H.: 34,8 mm; J, MNHN.F.A71416 (coll. Faullummel), Auversien (Bartonien) de Dhuisy (Seine-et-Marne), H.: 36,9 mm; K, MNHN.F.A71417 (coll. Faullummel), Auversien (Bartonien) de Dhuisy (Seine-et-Marne), H.: 39,5 mm; L, MNHN.F.A71418 (coll. Pacaud), Lutétiende Fontenayen-Vexin, Bois du But (Eure), protoconque. Échelle: L, 2 mm.
FIG. 8 in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 8. — Diagrammededispersiondurapportentrehauteuretdiamètremaximaldesespèces Cryptochorda (s.str.) stromboides (Hermann, 1781) () et Cryptochorda (s.str.) altavesna n. sp. ().
FIG. 7. — A-J in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 7. — A-J, Cryptochorda (s.str.) altavesna n. sp. A, B, F-H, Lutétiende Authevernes (Eure); C, D, Lutétiende Parnes (Oise); E, Lutétiende Maulette (Yvelines); I, J, Lutétiende Fontenay-en-Vexin, Bois du But (Eure). A, Holotype MNHN.F.A71419 (coll. Sautereau), H.: 44,8 mm; B, paratype MNHN.F.A71420 (coll. Sautereau), H.: 42,8 mm; C, MNHN.F.A71421 (coll. de Roissy), H.: 43,1 mm; D, MNHN.F.A71422 (coll. de Roissy), H.: 40,2 mm; E, MNHN.F.A71428 (coll. Sautereau), H.: 40,8 mm; F, paratype MNHN.F.A71423 (coll. Sautereau), H.: 46,0 mm; G, spécimen juvénile, paratype MNHN.F.A71424 (coll. Sautereau), H.: 22,2 mm; H, spécimen juvénile, paratype MNHN.F.A71425 (coll. Sautereau), H.: 26,4 mm; I, MNHN.F.A71440 (coll. Pacaud), H.: 7,1 mm; J, MNHN.F.A74441 (coll. Pacaud), protoconque. Échelle: J, 2 mm.
FIG. 9 in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 9. — Motifs colorés résiduels révélés sous lumière UV sur des spécimens juvéniles et adultes. A-O, Cryptochorda (s.str.) altavesna n. sp. A-F, Lutétien de Fontenay-en-Vexin, Bois du But (Eure); G, I, K-M, Lutétiende Parnes (Oise); H, J, N, Lutétien de Authevernes (Eure); O, Lutétien de Maulette (Yvelines); P, Cryptochorda(s.str.) stromboides (Hermann, 1781), Lutétiende Damery (Marne). A, MNHN.F.A71434 (coll. Pacaud), H.: 6,8 mm; B, MNHN.F.A71435 (coll. Pacaud), H.: 9,4 mm; C, MNHN.F.A71436 (coll. Pacaud), H.: 10,7 mm; D, MNHN.F.A71437 (coll. Pacaud), H.: 16,2 mm; E, MNHN.F.A71438 (coll. Pacaud), H.: 10,3 mm; F, MNHN.F.A71439 (coll. Pacaud), H.: 18,5 mm; G, MNHN.F.A71429 (coll. de Roissy), H.: 32,7 mm; H, Paratype MNHN.F.A71426 (coll. Sautereau), H.: 32,3 mm; I, MNHN.F.A71430 (coll. de Roissy), H.: 36,6 mm; J, Paratype MNHN.F.A71427 (coll. Sautereau), H.: 42,5 mm; K, MNHN.F.A71431 (coll. de Roissy), H.: 28,9 mm; L, MNHN.F.A71421 (coll. de Roissy), H.: 43,1 mm; M, MNHN.F.A71422 (coll. de Roissy), H.: 40,2 mm; N, Paratype MNHN.F.A71432 (coll. Sautereau), H.: 42,1 mm; O, MNHN.F.A71428 (coll. Sautereau), H.: 40,8 mm; P, MNHN.F.A71409 (coll. Staadt), H.: 51,6 mm.
FIG. 5. — A in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 5. — A, Sycostoma bulbus (Solander in Brander, 1766) [synonyme de Fusus bulbiformis Lamarck, 1803]. Figure originale du Pyrum arescens vel rugosum publiéepar Martini (1777) dansson Neuessystematisches Conchylien-Cabinet; B, Cryptochorda (s.str.) stromboides (Hermann, 1781). Figureoriginalede Strombus arescens publiéepar Pusch (1837) dansson Polens Paläontologie.
FIG. 1 in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 1. — Répartitiongéographique des taxaétudiés: A, bassinde Paris; B, Cotentin; C, Loire-Atlantique; D, bassin d'Aquitaine (voir Cadre géographique).
FIG. 4 in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 4. — Quelques figurations anciennes de Cryptochorda (s.str.) stromboides (Hermann, 1781): A, « Rustiques figulines » post-palisséenne, pièce de vaisselle décorative, non culinaire, à décor animalier comportant des moulages de coquilles dont quatre Cryptochorda (s.str.) stromboides (The Metropolitan Museum of Art/n°53.225.52). Dimensions: 52,1 x 39,7 x 7,1 cm; B, « Buccinites » in Seba (1765); C, « Voile d'artimon rougeatre » in Knorr (1768); D, « Buccinites » in Walch (1768); E, « Pyrum albidum arescens vel rugosum » in Martini (1777); F, in Favanne de Montcervelle (1780); G, in Buc'hoz (1778); H, in Schröter (1785).
FIG. 3. — A in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 3. — A, Notes manuscrites de Jean Hermann sur les premières pages blanches de son exemplaire de L'histoire naturelle éclaircie dans deux de ses parties principales. L'Oryctologie, qui traite des terres, des pierres, des métaux, des minéraux et autres fossiles de Dezallier d'Argenville, publié en 1755 (Bibliothèque de l'Université de Strasbourg); B, notes manuscrites de Jean Hermann sur les premières pages blanches de son exemplaire de L'histoire naturelle éclaircie dans deux de ses parties principales. La lithologie et la conchyliologie […] de Dezallier d'Argenville, publié en 1742 (Bibliothèque de l'Université de Strasbourg); C, figure originale du Buccinum stromboides (figs 5, 6) publiée par Jean Hermann en 1781 dans la revue allemande Der Naturforscher.
FIG. 2 in Contribution des motifs colorés résiduels dans la discrimination d'espèces nouvelles de Cryptochorda Mörch 1858 Mollusca: Gastropoda: Harpidae de l'Éocène du bassin de Paris et du Cotentin
FIG. 2. — Portrait de Jean Hermann (1738-1800), dessiné par Charles Guerrin et gravé par Ambroise Tardieu (frontispice des Observationes zoologicae publié par Hermann en 1804).
Amyloid-motif-dependent tau self-assembly is modulated by isoform sequence context
<p><span>The microtubule-associated protein tau is implicated in neurodegenerative diseases characterized by amyloid formation. Mutations associated with frontotemporal dementia increase tau aggregation propensity and disrupt its endogenous microtubule-binding activity. However, the structural relationship between aggregation propensity and biological activity remains unclear. We employed a multi-disciplinary approach, including computational modeling, NMR, cross-linking mass spectrometry, and cell models to engineer tau sequences that modulate its structural ensemble. Our findings show that substitutions near the conserved 'PGGG' </span><span>β</span><span>-turn motif informed by tau isoform context reduce tau aggregation in vitro and cells and can even counteract aggregation from disease-associated proline-to-serine mutations. Engineered tau sequences maintain microtubule binding and explain why 3R isoforms exhibit reduced pathogenesis compared to 4R. We propose a simple mechanism to reduce the formation of pathogenic tau species while preserving biological function, thus offering insights for therapeutic strategies aimed at reducing tau protein misfolding in neurodegenerative diseases.</span></p> <p><strong>Description of Source Data and Supplementary Data</strong>: All MD, NMR (peptide and tauRD), ThT, XL-MS, MT stabilization, MT:tau modeling, and cell-based aggregation data are available in the Source_Data directory as Data S1, Data S2, Data S3, Data S4, Data S5, Data S6, Data S7, and Data S8, respectively. Supplementary Data for raw MD trajectory files, structure files for MSM modeling and validation file, and tau:MT modeling are available as "Supplementary_Data_MD_Trajectories_Structures", "Supplementary_Data_MSM_models_Structures" and "Supplementary_Data_MT-tau_complex_models", respectively."</p>
Stable motifs delay species loss in simulated food webs
<p>Some three-species motifs (unique patterns of interactions between three species) are both more stable when modelled in isolation and over-represented in empirical food webs. This suggests that these motifs may reduce extinction risk for species participating in them, ultimately stabilizing the food web as a whole. We test whether a species' time to extinction following a perturbation is related to its participation in stable and unstable motifs and assess how motif roles covary with a species' degree or trophic level. We found that species' motif roles are related to their times to extinction following a disturbance. Specifically, having a larger proportion of the motif role made up by the omnivory motif was associated with longer times to extinction, even though the omnivory motif is less stable than the others in when modelled in isolation. While motif roles were associated with extinction risk, they also varied strongly with degree and trophic level. This means that these simpler measures of a species' role may be sufficient to roughly predict which species are most vulnerable to disturbance (though motif roles can be used to refine these predictions), but that studies of species' motif participation can also reasonably comment on vulnerability to extinction. Previous research showed that certain motifs appear more frequently in stable webs; we show that this is at least in part because participating in these motifs provides protection from extinction.</p>
Data for: The CD4 transmembrane GGXXG and juxtamembrane (C/F)CV+C motifs mediate pMHCII-specific signaling independently of CD4-Lck interactions
<p>We previously reported that the transmembrane GGXXG motif co-arose with the cytoplasmic juxtamembrane (C/F)CV+C motif in eutherian (placental mammal) CD4 and that constituent residues therein evolve under purifying selection (Lee, et al., 2022). These data led us to discover that mutating these motifs together increased CD4-Lck association but reduced CD3z, Zap70, and Plcg1 phosphorylation levels as well as IL-2 production. Because these mutants preferentially localized CD4-Lck pairs to non-membrane raft fractions, one potential explanation for our results was that they impaired proximal signaling by sequestering Lck away from TCR-CD3. An alternative hypothesis is that the mutations directly impacted TCR-CD3 signaling because the wild type motifs play a Lck-independent role in signaling. Here we used a reductionist approach to discriminate between these possibilities (Lee, et al., 2023). Our current data lead us to conclude that: intracellular CD4-Lck interactions are not necessary for pMHCII-specific signal initiation; the GGXXG and (C/F)CV+C motifs are key determinants of CD4-mediated pMHCII-specific signal amplification; the GGXXG and (C/F)CV+C motifs exert their functions independently of direct CD4-Lck association. These data provide a mechanistic explanation for why residues within these motifs are under purifying selection. The results are also important to consider for biomimetic engineering of synthetic receptors.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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