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Fig. 6 in Asplenium danxiaense sp. nov. (Aspleniaceae, Aspleniineae), a new tetraploid fern species from Guangdong, China, based on morphological and molecular data
Fig. 6. Estimation of Asplenium danxiaense K.W.Xu sp. nov. genome size by flow cytometry. The internal control Zea mays L. cv. B73 has 1C = 2.3Gbp.
Fig. 3 in Asplenium danxiaense sp. nov. (Aspleniaceae, Aspleniineae), a new tetraploid fern species from Guangdong, China, based on morphological and molecular data
Fig. 3. Scale morphology of the new species and its affinities. A, E. Asplenium danxiaenseK.W.Xu sp. nov. B, F. A. pulcherrimum (Baker) Ching ex Tardieu. C, G. A. coenobiale Hance. D, H. A. cornutissimum X.C.Zhang & R.H.Jiang.
Molecular data from "Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)"
<p><strong>Phylogenetic_dataset.csv</strong>: Unfiltered DArTseq data used in phylogenetic analyses. Readable by 'dartR' (Gruber et al. 2018).</p> <p><strong>Population_dataset.csv</strong>: Unfiltered DArTseq data used in population-level analyses. Readable by 'dartR' (Gruber et al. 2018).</p> <p><strong>Reference.csv</strong>: Spreadsheet listing individuals included in molecular analyses. Includes vouchers, species, name of each sample in DArTseq data sets, and GenBank accession numbers (GB) for mitochondrial data. ABTC stands for Australian Biological Tissue Collection; AA and CCM for field numbers of uncatalogued specimens. Other collection acronyms follow Sabaj (2019). We refrain from assigning individuals that were not included in the molecular analyses to any given species.</p>
Simulation data on the growth of atmospheric molecular clusters and particles
<p>This data set contains output data from cluster population simulations performed with Atmospheric Cluster Dynamics Code (ACDC) model, which simulates the formation of clusters from atmospheric vapors and the growth of these clusters by further molecular and cluster-cluster collisions. The data can be used for investigating the formation and growth of atmospheric particles from inorganic and organic vapors.</p> <p>The data is output of a computational process model, and hence does not represent a specific time period or location. Simulation sets are calculated for a one or two-component system containing a quasi-unary inorganic compound representing a mixture of sulfuric acid and ammonia (SA) and/or oxidized organic vapors corresponding to a low volatility organic compound (LVOC) and an extremely-low volatility organic compound (ELVOC). The external conditions in the simulations correspond to those in the CLOUD (Cosmics Leaving Outdoor Droplets) chamber at temperature of 5 C°.</p> <p>Data are provided for 14 simulations.</p> <p><strong>References</strong></p> <p>Kontkanen J, Stolzenburg D, Olenius T, Yan C, Dada L, Ahonen L, Simon M, Lehtipalo K, Riipinen I (2022) What controls the observed size-dependency of the growth rates of sub-10 nm atmospheric particles?. Environ. sci. Atmos. <a href="https://doi:10.1039/d1ea00103e">https://doi:10.1039/d1ea00103e</a> </p> <p>Olenius T, Riipinen I (2017) Molecular-resolution simulations of new particle formation: Evaluation of common assumptions made in describing nucleation in aerosol dynamics models. Aerosol Sci. Tech. 51:397 – 408. <a href="https://doi.org/10.1080/02786826.2016.1262530">https://doi.org/10.1080/02786826.2016.1262530</a></p> <p>Olenius T, Atmospheric Cluster Dynamics Code. <a href="https://github.com/tolenius/ACDC">https://github.com/tolenius/ACDC</a> </p> <p>McGrath MJ et al. (2012) Atmospheric Cluster Dynamics Code: a flexible method for solution of the birth-death equations. Atmos. Chem. Phys. 12:2345 – 2355. <a href="https://doi.org/10.5194/acp-12-2345-2012">https://doi.org/10.5194/acp-12-2345-2012</a></p> <p><strong>Data description</strong></p> <p>The data is in the form of text files. The provided data files (total compressed size ~10GB) correspond to simulation output from the ACDC model. Simulation sets are shown in the table below and further described in Kontkanen et al. (2022). For the interpretation of the model output, the interested user is referred to the manual of ACDC model (<a href="https://github.com/tolenius/ACDC">https://github.com/tolenius/ACDC</a>). </p> <table align="left"> <tbody> <tr> <td> <p>Simulation set</p> </td> <td> <p>Model compounds</p> </td> <td> <p>Vapor concentrations (cm<sup>-3</sup>)</p> </td> <td> <p>Method to retrieve evaporation rates</p> </td> </tr> <tr> <td> <p>1</p> </td> <td> <p>SA</p> </td> <td> <p><em>C</em><sub>SA </sub>= 8.0*10<sup>6</sup>, 2.0*10<sup>7</sup>, 4.7*10<sup>7</sup>, 1.1*10<sup>8</sup></p> </td> <td> <p>Kelvin eq.<br> <em>(classical evaporation rates)</em></p> </td> </tr> <tr> <td> <p>2</p> </td> <td> <p>SA</p> </td> <td> <p><em>C</em><sub>SA </sub>= 2.0*10<sup>7</sup>, 4.7*10<sup>7</sup>, 1.1*10<sup>8</sup></p> </td> <td> <p>QC data and Kelvin eq.<br> <em>(non-classical evaporation rates)</em></p> </td> </tr> <tr> <td> <p>3</p> </td> <td> <p>LVOC</p> </td> <td> <p><em>C</em><sub>LVOC </sub>= 5.0*10<sup>7</sup>, 1*10<sup>8</sup></p> </td> <td> <p>Kelvin eq.<br> <em>(classical evaporation rates)</em></p> </td> </tr> <tr> <td> <p>4</p> </td> <td> <p>LVOC,<br> ELVOC</p> </td> <td> <p><em>C</em><sub>LVOC </sub>= 5.0*10<sup>7</sup>, 1*10<sup>8</sup><br> <em>C</em><sub>ELVOC </sub>= 1.0 *10<sup>7</sup></p> </td> <td> <p>Kelvin eq.<br> <em>(classical evaporation rates)</em></p> </td> </tr> <tr> <td> <p>5</p> </td> <td> <p>LVOC,<br> SA</p> </td> <td> <p><em>C</em><sub>LVOC </sub>= 2.0*10<sup>7</sup>, 5.0*10<sup>7</sup>, 1*10<sup>8</sup><br> <em>C</em><sub>SA </sub>= 8.0*10<sup>6</sup></p> </td> <td> <p>Kelvin eq.<br> <em>(classical evaporation rates)</em></p> </td> </tr> </tbody> </table> <p> </p>
Fig. 2 in Molecular Data Confirm The Species Status Of Neoechinorhynchus Personatus And N. Yamagutii (Acanthocephala, Neoechinorhynchidae) From The Atlantic And Pacific Grey Mullets (Teleostei, Mugilidae)
Fig. 2 Phylogenetic tree of Neoechinorhynchus species obtained with maximum likelihood (ML) method (− ln likelihood 1619.55) based on the 18S rRNA partial gene sequences. Floridosentis mugilis was used as an outgroup. The ML/neighborn joining/minimum evolution bootstrap support is shown at each internal node.
Fig. 1 in A New Record Of Chaunocephalus Ferox (Digenea, Echinostomatidae) From Ciconia Nigra In Ukraine Including Morphological And Molecular Data
Fig. 1. Chaunocephalus ferox: 1— ventral view; 2 — head collar; 3 — head collar of hologenophore; 4 — uroproct.
Data supporting the study "The impact of molecular self-organisation on the atmospheric fate of a cooking aerosol proxy" by Milsom et al.
<p>Model and experimental data from the study "The impact of molecular self-organisation on the atmospheric fate of a cooking aerosol proxy" to be published in Atmospheric Chemistry and Physics. </p>
Fig 5 in Taxonomic Position Of Anastrangalia Reyi And A. Sequensi (Coleoptera, Cerambycidae) Based On Molecular And Morphological Data
Fig 5. Male aedeagi (A–D) and parameres (E–H) of A. reyi (A, E), A. sequensi (B, F), A. dubia (C, G) and A. sanguinolenta (D, H).
Fig. 1 in Taxonomic Position Of Anastrangalia Reyi And A. Sequensi (Coleoptera, Cerambycidae) Based On Molecular And Morphological Data
Fig. 1. Distribution of nucleotide substitutions within haplogroups: A — A. reyi (ArEu) (KJ964792); B — A. sequensi (AsFe) (KY683642); C — A. dubia (AdAl) (KM439943); D — A. dubia (AdPy) (KM285974). The unic nucleotide substitutions are red circled; the common substitutions are blue marked.
Fig. 3 in Taxonomic Position Of Anastrangalia Reyi And A. Sequensi (Coleoptera, Cerambycidae) Based On Molecular And Morphological Data
Fig. 3. Detailed phylogenetic subtree for the dubia group (hybrids of A. reyi and A. dubia are indicated by arrows).
Data from: Leme et al. (2022) New genera and a new species in the "Cryptanthoid Complex" (Bromeliaceae: Bromelioideae) based on the morphology of recently discovered species, seed anatomy, and improvements in molecular phylogeny. Phytotaxa (doi: 10.11646/phytotaxa.544.2.2)
<p>DNA sequence alignments as well as the input and output files which specify the different data partitioning schemes used for phylogenetic analyses in Leme et al. (2022) New genera and a new species in the “Cryptanthoid Complex” (Bromeliaceae: Bromelioideae) based on the morphology of recently discovered species, seed anatomy, and improvements in molecular phylogeny. Phytotaxa. (doi: 10.11646/phytotaxa.544.2.2)</p>
Data of curvature model for the study of nanoparticle size effects on amyloid fibril stability and molecular dynamics simulations data
<p>The data provided refer to our published article:</p> <p>T. John, J. Adler, C. Elsner, J. Petzold, M. Krueger, L.L. Martin, D. Huster, H.J. Risselada, B. Abel, Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation, J. Colloid Interface Sci. 622 (2022), 804–818. <a href="https://doi.org/10.1016/j.jcis.2022.04.134">https://doi.org/10.1016/j.jcis.2022.04.134</a></p> <p>This article is accompanied by a 'Data in Brief' article that explains in more detail the use of the curvature model and our molecular dynamics (MD) simulations:</p> <p>T. John, L.L. Martin, H.J. Risselada, B. Abel, Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data, Data Brief 45 (2022), 108598. <a href="https://doi.org/10.1016/j.dib.2022.108598">https://doi.org/10.1016/j.dib.2022.108598</a></p>
Fig. 1 in Molecular Data Confirm The Species Status Of Neoechinorhynchus Personatus And N. Yamagutii (Acanthocephala, Neoechinorhynchidae) From The Atlantic And Pacific Grey Mullets (Teleostei, Mugilidae)
Fig. 1 Phylogenetic tree of Neoechinorhynchus from grey mullets and across localities in the North-East Atlantic, Mediterranean and Japan Sea obtained with maximum likelihood (ML) method (− ln likelihood 1242.96) based on the 18S rRNA partial gene sequences. Floridosentis mugilis was used as an outgroup. The ML/neighborn joining/ minimum evolution bootstrap support is shown at each internal node. Identification number of isolates is as in table 1.
Fig. 5 in Taxonomic status of genera of Buccininae (Neogastropoda, Buccinidae) updated based on molecular data with description of new species and corrections of nomenclature of Buccinum
Fig. 5. Buccinum bizikovi sp. nov. A–B. Holotype (ZIN 62781), SL 20.0 mm. C. Paratype (ZIN 62782), SL 20.0 mm, lateral view to show the penis. D. South-eastern Sakhalin, depth 78 m, SL 21.5 mm, ZIN 62783. E–F. Buccinum ovulum Dall, 1895 (ZIN 48103), Kurile Is, Iturup I., depth 605–620 m, SL 16.9 mm. G. Holotype (USNM 106997), Aleutian Is, Andreanof Is, Amukta Pass, depth 454 m, SL 25.6 mm. Photo G: courtesy of USNM.
Fig. 6 in Taxonomic status of genera of Buccininae (Neogastropoda, Buccinidae) updated based on molecular data with description of new species and corrections of nomenclature of Buccinum
Fig. 6. Buccinum hasegawai sp. nov. (A–C) and Buccinum bizikovi sp. nov. (D–F). A–B. Paratype (ZIN 62777), SL 16.5 mm. A. Radula. B. Operculum. C. Paratype (ZIN 62782), penis. D. Paratype (ZIN 62782), SL 16.5 mm, radula. E. Paratype (ZIN 62782), SL 19.1 mm, operculum. F. Paratype (ZIN 62782), SL 16.5 mm, penis. Scale bars: C, F = 1 mm.
Fig. 1 in Taxonomic status of genera of Buccininae (Neogastropoda, Buccinidae) updated based on molecular data with description of new species and corrections of nomenclature of Buccinum
Fig. 1. Part of the Bayesian phylogenetic tree of Buccinoidea Rafinesque, 1815 obtained with the cox- 1, 16S and 28S concatenated dataset representing family Buccinidae Rafinesque, 1815. The full tree is available as supplementary material (Supplementary file 1). Subfamily Siphonaliinae Finlay, 1928 is collapsed. Vertical numbered lines on the right mark the subfamilies of Buccinidae: 1 = Beringiinae Golikov & Starobogatov, 1975; 2 = Neptuneinae Stimpson, 1865; 3 = Volutopsinae Habe & Sato, 1973; 4 = Parancistrolepidinae Habe, 1972. Posterior probabilities and bootstrap values are shown for each medium supported node. Highly supported nodes are marked with black dots. The colors of the text refer to valid genus (orange = Volutharpa P. Fischer, 1856) and species referred to or morphologically attributable to formerly recognized (sub)genera of Buccininae: red = Thysanobuccinum Golikov & Gulbin in Golikov, 1980; blue = Ovulatibuccinum Golikov & Sirenko, 1988; green = Bathybuccinum Golikov & Sirenko, 1988.
Fig. 4 in Taxonomic status of genera of Buccininae (Neogastropoda, Buccinidae) updated based on molecular data with description of new species and corrections of nomenclature of Buccinum
Fig. 4. Buccinum hasegawai sp. nov. A–B. Holotype (ZIN 62775 (Buc274)), SL 18.5 mm. C. Paratype 1 (ZIN 62902 (Buc276)) from the type locality, SL 14.8 mm. D. Paratype 2 (MIMB 42300 (Buc273)), Urup I., 450–460 m, SL 14.7 mm. E. Paratype (ZIN 26228), Iturup I., 414 m, SL 16.1 mm. F. Paratype (ZIN 26228), Iturup I., 414 m, SL 16.2 mm, lateral view to show the penis. G. Buccinum bombycinum Dall, 1907 (ZIN 48100) Iturup I., 910–920 m, SL 15.3 mm. H–I. Syntype (USNM 1105311), Japan, Honshu I., Suruga Bay, 536 m, SL 23.9 mm. I = enlarged upper part of the shell to show the sculpture. Scale bars: A–H = same scale; I = 5 mm. Photos H–I: courtesy of USNM.
Fig. 2 in Taxonomic status of genera of Buccininae (Neogastropoda, Buccinidae) updated based on molecular data with description of new species and corrections of nomenclature of Buccinum
Fig. 2. Sequenced species of Buccinum Linnaeus, 1758 previously attributed to Thysanobuccinum Golikov & Gulbin in Golikov, 1980, Bathybuccinum Golikov & Sirenko, 1988 and Ovulatibuccinum Golikov & Sirenko, 1988. A–B. Buccinum tunicatum Golikov & Gulbin, 1977 (Buc265), Okhotsk Sea, off Urup I., depth 142 m, R/V Akademik Oparin, 56 cr., sta 7, SL 20.4 mm. C. Buccinum sp. 2 (Buc175), off Onagawa, Miyagi, Honshu I., Japan, depth 3302–3311 m, SL 20.3 mm. D–D'. Buccinum cf. tunicatum (Buc269), Okhotsk Sea coast of Urup I., 2 m, R/V Akademik Oparin, 56 cr., sta 26, SL 8.7 mm. D = at the same scale as others; D' = enlarged. E–E'. Buccinum bicordatum (Golikov & Sirenko, 1988) (Buc188), off Onagawa, Miyagi, Honshu I., Japan, depth 342–343 m, SL 8.4 mm. E = at the same scale as others; E' = enlarged. F. Buccinum unicordatum (Golikov & Sirenko, 1988) (Buc266), Kurile Is, Iturup I., Prostor Bay, depth 264–270 m, SL 15.9 mm. G. Buccinum chinoi nom. nov. (Buc190), off Onagawa, Miyagi, Honshu I., Japan, depth 342–343 m, SL 9.0 mm. H. Buccinum fimbriatum (Golikov & Sirenko, 1988) (Buc275), Kurile Is, Simushir I., depth 436 m, R/V Akademik Oparin, 56 cr., stn 19, SL 16.6 mm. I. Buccinum sp. 1 (Buc189), off Onagawa, Miyagi, Honshu I., Japan, depth 342–343 m, SL 22.4 mm. All shells (except D', E') at the same scale.
Fig. 3 in Taxonomic status of genera of Buccininae (Neogastropoda, Buccinidae) updated based on molecular data with description of new species and corrections of nomenclature of Buccinum
Fig. 3. Sequenced species of Buccinum Linnaeus, 1758, Volutharpa P. Fischer, 1856, and Plicibuccinum Golikov & Gulbin, 1977. A. Buccinum tenuisulcatum Golikov & Gulbin, 1977 (Buc264), Okhotsk Sea, Kurile Is, Onekotan I., depth 571–580 m, R/V Akademik Oparin, 56 cr., stn 68, SL 29.4 mm. B. Buccinum cyaneum Bruguière, 1789 (Buc281), Barents Sea, Teriberka Inlet, depth 10–17 m, SL 18.1 mm. C–D. Volutharpa ampullacea (Middendorff, 1848) (Buc277), Kurile Is, off Chirpoi I., depth 148–147 m, SL 14.1 mm. E. Buccinum nipponense Dall, 1907 (Buc187), off Otsuchi, Iwate, Honshu I., Japan, depth 479–484 m, SL 40.8 mm. F. Buccinum percrassum Dall, 1883 (Buc283), Kurile Is, Simushir I., 1–6 m, SL 33.5 mm. G–H. Buccinum cf. kobjakovae Golikov & Gulbin, 1977 (Buc278), Kurile Is, Simushir I., R/V Akademik Oparin, 56 cr., stn 19, 46°40.6′ N, 151°58.4′ E, depth 436 m, SL 12.1 mm. I. Plicibuccinum declivis (Habe & Ito, 1976) (Buc289), Japan Sea, Primorje, R/V Akademik Oparin, 64 cr., stn 73, 43°43.5′ N, 135°22.9′ E, depth 45–49 m, SL 36.2 mm. Shells not to scale.
Data for FEgrow: An Open-Source Molecular Builder and Free Energy Preparation Workflow
<p>Data illustrating the use of de novo design in building and scoring protein-ligand complexes.</p> <p>This is relationship to the FEgrow publication with the intiial preprint here: <br> https://chemrxiv.org/engage/chemrxiv/article-details/6287bb98a42e9c78d34769f6<br> </p> <p>The FEgrow software snapshot used can be found here: https://zenodo.org/record/7105647#.YzFwINLMIUE</p>
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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.