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Supplementary material 2 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Table S2. Taxonomic composition and clustering of the mock community sample.: Explanation note: Taxonomic composition and clustering of the mock community sample.
Supplementary material 1 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The sequences renamed during the workshop. The INSDC accession number, the original INSDC name, and the new UNITE name are shown :
Supplementary material 3 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The metadata annotations for the sequences that were found in the same SHs as sequences from the built environment :
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 0% (0 molecules), 10 % (22 molecules), 20 % (50 molecules), or 30 % (86 molecules) of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p>*** IMPORTANT ***</p> <p>This is a correction to an earlier dataset simulated with some missing dihedrals, see: DOI: 10.5281/zenodo.61649</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</p>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field.
<p>Simulations of a POPC bilayer with varying amounts<br> of cholesterol. This data is employed for the NMRlipids<br> project, see <em>http://nmrlipids.blogspot.fi</em> for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 0% (0 molecules), 10 %<br> (22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br> of cholesterol. The Slipids model [1–3] is employed for lipids,<br> and the tip3p model for water.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. Additionally,<br> the initial structure (.gro), topology (.top), index file (.ndx),<br> binary run input file for GROMACS v. 4.6–> (.tpr) and the<br> energy output file (.edr) are provided together with the run<br> parameter file (.mdp) employed to run all the simulations.</p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
text-fig. 24. Anterior theropod cervical vertebrae in lateral view, illustrating several cervical characters, a, Herrerasaurus ischigualastensis; redrawn from Sereno and Novas (1993). B, Lilienstemus lilienstemi; based on MB R. 2175. c, Dilophosaurus wetherillv, based on UCMP V 6468. D, Allosaurus fragilisa based on Madsen (1976) and MOR 693. Abbreviations: di, diapophysis; ep, epipophysis; k, keel; ns, neural spine; pl, pleurocoel; poz, postzygapophysis; pp, parapophysis; prz, prezygapophysis. Scale bars represent 10 mm (a-b) and 50 mm (c-d). in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 24. Anterior theropod cervical vertebrae in lateral view, illustrating several cervical characters, a, Herrerasaurus ischigualastensis; redrawn from Sereno and Novas (1993). B, Lilienstemus lilienstemi; based on MB R. 2175. c, Dilophosaurus wetherillv, based on UCMP V 6468. D, Allosaurus fragilisa based on Madsen (1976) and MOR 693. Abbreviations: di, diapophysis; ep, epipophysis; k, keel; ns, neural spine; pl, pleurocoel; poz, postzygapophysis; pp, parapophysis; prz, prezygapophysis. Scale bars represent 10 mm (a-b) and 50 mm (c-d).
Table S.2 - List of taxa of the 10,000 species included in the k-mean analysis
<p>Oteiza, M (2019). Table S.2 - List of taxa of the 10,000 species included in the k-mean analysis. MSc Thesis. Universidad Internacional Menéndez Pelayo</p>
FIGURE 10. Rhynchosia species. A, B. R. lineata. C–F. R. mantaroensis var. cuprinervia. G–J. R. melanocarpa. K–N. R in Taxonomic revision of Rhynchosia Lour. (Leguminosae, Papilionoideae, Phaseoleae) in South America
FIGURE 10. Rhynchosia species. A, B. R. lineata. C–F. R. mantaroensis var. cuprinervia. G–J. R. melanocarpa. K–N. R. minima. (A, B by A. Mailhos); (C–F by R. Ripley) and (G–N by T. C. Monteiro).
FIGURE 10. A–K. Goniozus nephoterycis Kurian, 1952. Holotype. A in Rediscovery of Kurian's types of Hymenoptera at Forest Research Institute, Dehradun, India with notes on Indian bethylid fauna
FIGURE 10. A–K. Goniozus nephoterycis Kurian, 1952. Holotype. A. Habitus, lateral view; B. Head, frontal view; C. Head, lateral view; D. Antenna; E. Mesosoma, dorsal view; F. Mesosoma, lateral view; G. Posterior half of mesonotum and Metapectalpropodeal disc, dorsal view; H. Forewing; I. Legs (left to right) pro- and metalegs; J. Two slides of holotype; K. Labels.
FIGURE. Fruits of the genera and subgenera of Bromelioideae. A. Acanthostachys pitcairnioides (Leme 483). B. Acanthostachys strobilacea (Leme 8306). C. Aechmea subg. Platyaechmea s.str.: A. caesia (Leme 3588). D. Aechmea subg. Lamprococcus: A capixabae (Leme 6948). E. Aechmea of the "Streptocalycoid complex": A. nidularioides (Leme 2150). F. Wittmackia lingulatoides (Leme 9585). G–H. Aechmea of the "Gravisia complex". G. A. aquilega (Leme 9516). H. A. blanchetiana (Leme 8890). I–L. Aechmea subg. Chevaliera s.l. I. A. castanea (Leme 6940). J. A. digitata (Leme 4019). K. A. fernandae (Leme 4492). L. A. ornata (Leme 6760). M. Greigia stenolepis (Leme 9738). N. Bromelia antiacantha (Leme 258). O. Bromelia aff. reversacantha (Leme 4609). P–Q. Billbergia subg. Billbergia. P. B. amoena var. amoena (Leme 6168). Q. B. amoena var. stolonifera (Leme 215-B). R. Billbergia subg. Helicodea: B. zebrina (Leme 128). S. Cryptanthus tabuleiricola (Leme 8014). T. Billbergia (Pseudaechmea) viridiflora (SEL 99-026). U. Portea petropolitana var. noetiigii (Leme 5277). V. Hohenbergia lanata (Leme 9625). W. Quesnelia quesneliana (Leme 107). X. Fernseea bocainensis (Leme 1422). Y. Disteganthus lateralis (Leme 9390). Z. Neoglaziovia variegata (Leme 9631). a. Aechmea subg. Pothuava s.l.: A. roberto-seidelii (Leme 1203). b. Aechmea subg. Macrochordion: A. bruggeri (Leme 4765). c. Araeococcus flagellifolius (Leme 9501). Bars = 10 mm. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Fruits of the genera and subgenera of Bromelioideae. A. Acanthostachys pitcairnioides (Leme 483). B. Acanthostachys strobilacea (Leme 8306). C. Aechmea subg. Platyaechmea s.str.: A. caesia (Leme 3588). D. Aechmea subg. Lamprococcus: A capixabae (Leme 6948). E. Aechmea of the "Streptocalycoid complex": A. nidularioides (Leme 2150). F. Wittmackia lingulatoides (Leme 9585). G–H. Aechmea of the "Gravisia complex". G. A. aquilega (Leme 9516). H. A. blanchetiana (Leme 8890). I–L. Aechmea subg. Chevaliera s.l. I. A. castanea (Leme 6940). J. A. digitata (Leme 4019). K. A. fernandae (Leme 4492). L. A. ornata (Leme 6760). M. Greigia stenolepis (Leme 9738). N. Bromelia antiacantha (Leme 258). O. Bromelia aff. reversacantha (Leme 4609). P–Q. Billbergia subg. Billbergia. P. B. amoena var. amoena (Leme 6168). Q. B. amoena var. stolonifera (Leme 215-B). R. Billbergia subg. Helicodea: B. zebrina (Leme 128). S. Cryptanthus tabuleiricola (Leme 8014). T. Billbergia (Pseudaechmea) viridiflora (SEL 99-026). U. Portea petropolitana var. noetiigii (Leme 5277). V. Hohenbergia lanata (Leme 9625). W. Quesnelia quesneliana (Leme 107). X. Fernseea bocainensis (Leme 1422). Y. Disteganthus lateralis (Leme 9390). Z. Neoglaziovia variegata (Leme 9631). a. Aechmea subg. Pothuava s.l.: A. roberto-seidelii (Leme 1203). b. Aechmea subg. Macrochordion: A. bruggeri (Leme 4765). c. Araeococcus flagellifolius (Leme 9501). Bars = 10 mm.
FIGURE. Pollen of Hylaeaicum and Aechmea aculeatosepala. A. H. eleutheropetalum (Leme 4491). B. H. eleutheropetalum var. bicolor (SEL 86-44). C. H. aff. myrmecophilum (Leme 3487). D. H. myrmecophilum (Leme 2555). E. H. levianum (Leme 2777). F. H. margaretae (Leme 2748). G. H. aff. myrmecophilum (Leme 2553). H. H. margaretae (Leme 2331). I. H. wurdackii (Leme 2567). J. H pendulum (Leme 1979). K. H. tarapotoense (Leme 1977). L. Aechmea aculeatosepala (Leme 3235). Bars = 10 µm. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Pollen of Hylaeaicum and Aechmea aculeatosepala. A. H. eleutheropetalum (Leme 4491). B. H. eleutheropetalum var. bicolor (SEL 86-44). C. H. aff. myrmecophilum (Leme 3487). D. H. myrmecophilum (Leme 2555). E. H. levianum (Leme 2777). F. H. margaretae (Leme 2748). G. H. aff. myrmecophilum (Leme 2553). H. H. margaretae (Leme 2331). I. H. wurdackii (Leme 2567). J. H pendulum (Leme 1979). K. H. tarapotoense (Leme 1977). L. Aechmea aculeatosepala (Leme 3235). Bars = 10 µm.
FIGURE. Flowers and longitudinal sections of ovaries of Hylaeaicum and Neoregelia. A–K. Hylaeaicum. A. H. eleutheropetalum (Leme 4491). B. H. myrmecophilum (Leme 2555). C. H. aff. myrmecophilum (Leme 3487). D. H. levianum (Leme 2777). E. H. wurdackii (Leme 2567). F. H. pendulum (Leme 1979). G. H. wurdackii (Leme 2567). H. H. aff. myrmecophilum (Leme 2553). I. H. pendulum (Leme 1979). J. H. eleutheropetalum (Leme 4491). K. H. levianum (Leme 5639-A) highlighting the immature seeds connected to the placenta. L–P. Neoregelia subg. Neoregelia. L–M. N. binotii (Leme 3482). N. N. ampullacea (Leme 9299). O–P. N. pontualii (Leme 5520). Q–S. Neoregelia subg. Longipetalopsis. Q–R. N. rubrovittata (Leme 1865). S. N. pernambucana (Leme 4407). Bars = 10 mm (A–F, L–S), 5 mm (G–K). in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Flowers and longitudinal sections of ovaries of Hylaeaicum and Neoregelia. A–K. Hylaeaicum. A. H. eleutheropetalum (Leme 4491). B. H. myrmecophilum (Leme 2555). C. H. aff. myrmecophilum (Leme 3487). D. H. levianum (Leme 2777). E. H. wurdackii (Leme 2567). F. H. pendulum (Leme 1979). G. H. wurdackii (Leme 2567). H. H. aff. myrmecophilum (Leme 2553). I. H. pendulum (Leme 1979). J. H. eleutheropetalum (Leme 4491). K. H. levianum (Leme 5639-A) highlighting the immature seeds connected to the placenta. L–P. Neoregelia subg. Neoregelia. L–M. N. binotii (Leme 3482). N. N. ampullacea (Leme 9299). O–P. N. pontualii (Leme 5520). Q–S. Neoregelia subg. Longipetalopsis. Q–R. N. rubrovittata (Leme 1865). S. N. pernambucana (Leme 4407). Bars = 10 mm (A–F, L–S), 5 mm (G–K).
FIGURE. Roussoella pseudohysterioides (GMB0009). a–d. Ascostromata developing on bamboo culm. e, f. Vertical sections of ascostromata. g–j. Asci containing eight ascospores. k. Fragment of ascostromata in KOH without stromatal pigments. l–m. Ascus apex in Melzer's reagent. n–r. Dark brown ascospores. Scale bars: j–r = 10 μm. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Roussoella pseudohysterioides (GMB0009). a–d. Ascostromata developing on bamboo culm. e, f. Vertical sections of ascostromata. g–j. Asci containing eight ascospores. k. Fragment of ascostromata in KOH without stromatal pigments. l–m. Ascus apex in Melzer's reagent. n–r. Dark brown ascospores. Scale bars: j–r = 10 μm.
FIGURE 10 in Review of Kamimuria (Plecoptera: Perlidae) from Zhejiang and Fujian provinces, China, with notes on the morphological variability of K. tienmushanensis Wu, 1938
FIGURE 10. Kamimuria tienmushanensis, male terminalia, dorsal. A–C: Longquan City, Zhejiang, D: Wuyi Mountains, Fujian, terga with lighter coloration.
Supplementary material 10 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Additional list of 52 persons who kindly provided their observations of red-eared sliders in open water bodies of Eurasia
FIGURE 10. Phelipanche pulchella. A–D. General habit. E–G. Flower, side view. H–J. Flower, front view. K, M in Holoparasitic Orobanchaceae in Georgia (Caucasus): taxonomic revision, diversity, distribution, habitats and host range
FIGURE 10. Phelipanche pulchella. A–D. General habit. E–G. Flower, side view. H–J. Flower, front view. K, M. Representative habitats in Borjomi (Samtskhe-Javakheti prov.). L. Host, Teucrium chamaedrys. Photos by R. Piwowarczyk.
FIGURE 10. Seed anatomy. A, C. Krenakanthus ribeiranus. B, D. K. roseolilacinus. A–B in A "hairy situation" in Minas Gerais, Brazil: a striking new species of Krenakanthus (Bromeliaceae: Bromelioideae) covered with uniseriate trichomes
FIGURE 10. Seed anatomy. A, C. Krenakanthus ribeiranus. B, D. K. roseolilacinus. A–B. Seeds in median cross-section. C–D. Detail of the seed coat in anti-raphe. Arrowhead: tegmic cuticle. ar = anti-raphe. en = endosperm. pr = pre-raphe. The numbers indicate the different seed coat layers. 1 = endotegmen. 2 = exotegmen. 3 = endotesta. 4 = exotesta. Bars: A–B = 200 μm. C–D = 50 μm.
Figures 10-15 from: Pawlęga K, Łętowski J, Szwaj E, Gosławski T (2019) The morphology of the immature stages of Squamapion atomarium (Kirby, 1808) (Coleoptera, Brentidae) and notes on its life cycle. ZooKeys 892: 143-160. https://doi.org/10.3897/zookeys.892.36027
Figures 10-15 Squamapion atomarium10 pupa 11 occurrence environment 12 a gall 13 the most common place to lay eggs at the root collar 14 place for laying eggs 15 larva in prepupal stage for pupation.
Figure 10 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 10 Principal components analysis (PCA) of P. discordans (red), P. omphalodes (blue) and P. pinnatifida (green), based on the bioclimatic factors from individuals.
Figure 10 from: Han H-Y, Ro K-E (2019) DNA barcoding reveals a species group of the genus Campiglossa (Diptera, Tephritidae, Tephritinae) with recognition of a new species from East Asia and previously unknown females of Campiglossa coei (Hardy). ZooKeys 899: 1-36. https://doi.org/10.3897/zookeys.899.46779
Figure 10 A Holotype male of Campiglossa favillacea Ito, 2011 (new synonym of C. coei, UOPJ) B from left, two paratype females and holotype of C. favillacea [UOPJ] C holotype female of C. roscida Ito, 2011 (new synonym of C. misella) D ditto E holotype or paratype male wing of C. pishanicaF holotype male wing of C. propriaE, F reproduced from Wang (1998) with permission from Xing-Jian Wang.
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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
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.