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Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level
<p>T-cell receptor sequencing (TCR-seq) was performed on enriched CD8+ T-cells. TCR clonotype annotation was performed using MiXCR v.3.0.13 with the default input parameters.</p> <p>Full origin and method description available in:<br>Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level</p>
FIG. 5. — Rhytidhysteron subrufulum X.-L in Multigene phylogenetic support for novel Rhytidhysteron Speg. species (Hysteriaceae) from Sichuan Province, China
FIG. 5. — Rhytidhysteron subrufulum X.-L. Xu & C.-L. Yang, sp. nov. (holo-, SICAU19-0010): A, appearance of apothecia on host; B, C, ascomata; D, vertical section of hysteriothecium; E, exciple; F, G, pseudoparaphyses; H-M, asci; N, ocular chamber; O-S, ascospores; T, germinated ascospores; U, colonies on PDA for five days. Scale bars: A, 1 mm; B, C, 0.5 mm; D, 200 μm; E, 50 μm; F-M, 20 μm; N-T, 10 μm.
FIG. 4. — Rhytidhysteron sichuanensis X.-L in Multigene phylogenetic support for novel Rhytidhysteron Speg. species (Hysteriaceae) from Sichuan Province, China
FIG. 4. — Rhytidhysteron sichuanensis X.-L. Xu & C.-L. Yang, sp. nov. (holo-, SICAU 19-0004): A, appearance of apothecia on host; B, C, ascomata; D, vertical section of hysteriothecium; E, exciple; F, pseudoparaphyses; G-K, asci; L, ocular chamber; M-P, ascospores; Q, germinated ascospores; R, colonies on PDA for six days. Scale bars: A, B, 1 mm; C, 0.5 mm; D, 200 μm; E-K, 20 μm; L-Q, 10 μm.
FIG. 3. — Rhytidhysteron ligustrum X.-L in Multigene phylogenetic support for novel Rhytidhysteron Speg. species (Hysteriaceae) from Sichuan Province, China
FIG. 3. — Rhytidhysteron ligustrum X.-L. Xu & C.-L. Yang, sp. nov. (holo-, SICAU 20-0004): A, appearance of apothecia on host; B, C, ascomata; D, vertical section of hysteriothecium; E, exciple; F, pseudoparaphyses; G-K, asci; L, ocular chamber; M, germinated ascospores; N-Q, ascospores; R, colonies on PDA for five days. Scale bars: A, 1 mm; B, C, 0.5 mm; D, 100 μm; E-K, 20 μm; L-Q, 10 μm.
FIG. 1 in Multigene phylogenetic support for novel Rhytidhysteron Speg. species (Hysteriaceae) from Sichuan Province, China
FIG. 1. — Phylogram generated from RAxML analyses based on combined LSU, SSU, ITS and tef-1α sequence dataset within the genus Rhytidhysteron Speg. The tree is rooted to Hysterographium fraxini (Pers.) De Not. (CBS 109.43 and MFLU 15-3681). ML ≥70% and BYPP ≥0.95 are defined as ML/BYPP above or below the nodes. The type strains are in bold and the newly generated sequences are highlighted in red.
FIG. 2 in Multigene phylogenetic support for novel Rhytidhysteron Speg. species (Hysteriaceae) from Sichuan Province, China
FIG. 2. — Rhytidhysteron hongheense Wanas (SICAU 19-0006): A, appearance of apothecia on host; B, C, ascomata; D, vertical section of hysteriothecium; E, F, exciple; G, pseudoparaphyses; H-K, asci; L, M, ocular chamber; N-P, ascospores; Q, germinated ascospores; R, colonies on PDA for four days. Scale bars: A, B, 1 mm; C, 0.5 mm; D, 200 μm; E-K, 20 μm; L-Q, 10 μm.
FIG. 14 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 14. — Halocryptovalsa salicorniae Dayarathne & K.D.Hyde, sp. nov. (MFLU 16-0551 – holotype): A, host (Salicornia sp.); B, C, appearance of ascostromata on host; D, horizontal section through ascostroma; E, section through neck region; F, peridium; G, H, asci; I, asci with paraphyses; J-M, ascospores; N, germinating ascospores; O, P, culture on PDA (O-upper, P-lower). Scale bars: B, 500 µm; D-F, 100 μm; G-I, 50 μm; J-N, 5 μm.
FIG. 11 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 11. — Cryptovalsa suaedicola Spooner (IMI139939 – holotype): A, B, herbarium material; C, appearance of stromata on host;D, horizontal section through stroma; E, section through stroma; F, neck region; G, peridium; H-I, asci; J, paraphyses; K-N, ascospores. Scale bars: C-E, 200 μm; F, 50 μm; G-J, 20 μm; K-N, 10 μm.
FIG. 7 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 7. — Cryptosphaeria bathurstensis (K.D.Hyde & Rappaz) Dayarathne & K.D.Hyde, comb. nov. (BRIP 78339 – holotype): A, herbarium material; B, horizontal section through ascostroma; C, appearance of ascostromata on host; D, section through ascoma; E, peridium; F-H, asci; I, paraphyses; J-N, ascospores. Scale bars: B, 500 μm; C, 1000 μm; D, 100 μm; E-H, 20 μm; I, 10 μm; J-N, 5 μm.
FIG. 5 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 5. — Sexual morph of Cryptosphaeria avicenniae Devadatha & V.V.Sarma, sp. nov. (AMH-9952 – holotype): A, ascomata erumpent, immersed in decaying wood of Avicennia marina; B, horizontal sections of ascomata; C, vertical section of ascomata; D, peridium; E-I, immature and mature asci; J, paraphyses; K-O, ascospores; P, germ tube develop from apical side of ascospore; Q, R, culture on PDA (Q-upper, R-lower). Scale bars: C, 100 μm; D, E, 50 μm; F-I, J, K = 20 μm; J, K, 20 μm; L-P, 5 μm.
FIG. 4 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 4. — Phylogram generated from the best scoring MP tree based on combined LSU and SSU sequence data. Bootstrap support values for maximum parsimony (MP) equal or greater than 60 % are given above the nodes. The tree is rooted to Xylaria hypoxylon (OCS 100004) and Xylaria acuta (5089). Scale bar: 50 (expected number of nucleotide substitutions per site per branch).
FIG. 13. — Eutypella naqsii K.D in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 13. — Eutypella naqsii K.D.Hyde (BRIP 22588, holotype). A, herbarium material; B, horizontal section through ascostroma; C, D, vertical section through ascoma; E, peridium; F, paraphyses; G-I, asci; J-N, ascospores. Scale bars: B, 1000 μm; C, 500 μm; D,100 μm; E, F-I, 20 μm; J, 10 μm; K-N, 5 μm.
FIG. 3 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 3. — Phylogram generated from the best scoring RAxML tree based on combined LSU and SSU sequence data. Bootstrap support values for maximum likelihood (ML, blue) equal or greater than 60 % are given above the nodes. Bayesian posterior probabilities (PP, green) equal or greater than 0.90 are shown above the branches. The tree is rooted to Xylaria hypoxylon (OCS 100004) and Xylaria acuta (5089). All sequences from ex-type strains are in bold. Scale bar: 0.02 (expected number of nucleotide substitutions per site per branch).
FIG. 17. — Pedumispora rhizophorae K.D.Hyde & E.B.G in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 17. — Pedumispora rhizophorae K.D.Hyde & E.B.G.Jones (BRIP 19201 – holotype): A, herbarium material; B, C, appearance of ascostromata on host; D, section through ascoma; E, section through neck region; F, peridium; G, paraphyses; H, I, asci; J, K, ascospores. Scale bars: B, 1000 μm; C, 500 μm; D, 50 μm; E-G, 20 μm; H-K, 100 μm.
FIG. 10 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 10. — Cryptovalsa mangrovei Abdel-Wahab & Inderb (IMI 379746 – holotype): A, B, herbarium material; C, D, appearance of stromata on host; E, section through ascoma; F, neck region; G, peridium; H paraphyses; I-L, asci; M, ascospores. Scale bars: C, 500 μm; D, 200 μm; E, F, 100 μm; G, H, M, 20 μm; I-K, 50 μm.
FIG. 2 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 2. — Phylogram generated from the best scoring RAxML tree based on ITS sequence data. Bootstrap support values for maximum likelihood (ML, black) and maximum parsimony (MP, blue) equal or greater than 60% are given above the nodes. Bayesian posterior probabilities (PP, green) equal or greater than 0.90 are shown above the branch. The tree is rooted to Xylaria hypoxylon (CBS 122620) and Kretzschmaria deusta (CBS 826.72). Scale bar: 0.09 (expected number of nucleotide substitutions per site per branch).
FIG. 16 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 16. — Halodiatrype mangrovei (K.D.Hyde) Dayarathne & K.D.Hyde (BRIP 19869 – holotype); A, herbarium material; B, C, appearance of ascomata on host surface; D-F, vertical section through ascoma; G, vertical section through neck region; H, peridium; I, paraphyses; J-L, asci; M-P, ascospores. Scale bars: B, E, F, 500 μm; C, 1000 μm; D, 200 μm; G, 50 μm; H, K-L, 20 μm; M-P, 10 μm.
FIG. 1 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 1. — Phylogram generated from the best scoring RAxML tree based on combined ITS and Btub sequence data. Bootstrap support values for maximum likelihood (ML, black) and maximum parsimony (MP, blue) equal or greater than 60 % are given above the nodes. Bayesian posterior probabilities (PP, green) equal or greater than 0.90 are shown above the branch. The tree is rooted to Xylaria hypoxylon (CBS 122620) and Kretzschmaria deusta (CBS 826.72). All sequences from ex-type strains are in bold. Symbols:, polysporous species;, octosporous species;, species with less than eight spores. Scale bar: 0.2 (expected number of nucleotide substitutions per site per branch).
FIG. 12 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 12. — Diatrype mangrovei Dayarathne & K.D.Hyde, sp. nov. (MFLU 17-0412 – holotype): A, appearance of ascostromata on host (Bruguiera cylindrica); B, horizontal section through ascostroma; C, section through ascoma; D, peridium; E-G, asci; H, ascospores; I, germinating ascospore; J, K, culture on PDA (J-upper, K-lower). Scale bars: A, 500 µm; B, 500 μm; C, 100 μm; D-G, 50 μm; H, I, 10 μm.
FIG. 8 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 8. — Cryptosphaeria halophila Dayarathne & K.D.Hyde, sp. nov. (MFLU 16-1199 – holotype): A, host (Avicennia sp.); B, horizontal section through conidioma; C-E, conidiophores and conidiogenous cells; F-I, conidia. Scale bars: A, 100 μm; B-E, 50 μm; F-I, 20 μm.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.