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The introduction of R
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Turek Laboratory Sleep-Wake Dataset and R Code for Analysis
<p>Sleep-wake dataset for MCI-Park mice and R code used for statistical analysis. </p>
FIGURE 1. Raphiocarpus bicallosus. A. Intact flowering shoot. B. Flattened plant parts. C, D. Internodes and prophylls. E. Leaf petiole. F in The checklist of Raphiocarpus species (Gesneriaceae, Didymocarpinae) in the flora of Vietnam with the description of a new species, R. bicallosus
FIGURE 1. Raphiocarpus bicallosus. A. Intact flowering shoot. B. Flattened plant parts. C, D. Internodes and prophylls. E. Leaf petiole. F. Leaves, adaxial and abaxial side. G. Median part and margin of the leaf blade, adaxial surface. H. Peduncle. I. Young inflorescence. J. Intact inflorescences. K. Flower buds and flowers, side and half-side views. L. Calyx segments. M. Intact perianth, frontal view. N. Perianth tube, views outside and inside with details of stamens and staminodia. O. Pistil. P. Distal part of pistil and stigma. Q. Ripening fruit. All photos made from the plant used for the type preparation, NHC 20211124004. Photos, correction, and plate design by Cuong Huu Nguyen and L. Averyanov.
FIGURE 2. Raphiocarpus bicallosus. A. Habit. B in The checklist of Raphiocarpus species (Gesneriaceae, Didymocarpinae) in the flora of Vietnam with the description of a new species, R. bicallosus
FIGURE 2. Raphiocarpus bicallosus. A. Habit. B. Leaves, adaxial and abaxial side. C, D. Internodes and prophylls. E. Flower buds and flowers, side and half-side views. F. Intact perianth, frontal view. G. Perianth tube, views outside and inside with details of stamens and staminodia. H. Calyx segments. I. Pistil and stigma. Drawn by Kien C.N. from the holotype NHC 20211124004.
FIGURES 4a–o in Song dialects as diagnostic characters - acoustic differentiation of the Canary Island Goldcrest subspecies Regulus regulus teneriffae Seebohm 1883 and R. r. ellenthalerae Päckert et al. 2006 (Aves: Passeriformes: Regulidae)
FIGURES 4a–o. Territorial song of Regulus regulus teneriffae, song types indicated on the sonagrams, lower left. La Gomera: a–d, song type A, strophes of four different males; Tenerife: e, g–h, song type A1 withfixed motiv I, strophes of three different males; f, rare song type F; i, song type B, male from Esperanza Forest; k–m, song type B, three different males from Anaga Mts; n, song type C, male from Anaga Mts; o, song type D, male from Anaga Mts.
FIGURE 2 in Song dialects as diagnostic characters - acoustic differentiation of the Canary Island Goldcrest subspecies Regulus regulus teneriffae Seebohm 1883 and R. r. ellenthalerae Päckert et al. 2006 (Aves: Passeriformes: Regulidae)
FIGURE 2. Distribution of Gold and Firecrests on the Atlantic islands. Distribution of dialect song types from the Canary Islands is indicated by symbols on the according island.
FIGURES 1a–d in Song dialects as diagnostic characters - acoustic differentiation of the Canary Island Goldcrest subspecies Regulus regulus teneriffae Seebohm 1883 and R. r. ellenthalerae Päckert et al. 2006 (Aves: Passeriformes: Regulidae)
FIGURES 1a–d. Vocalization pattern of Goldcrests; a, bipartite song of European Goldcrests, R. r. regulus, Czech Republik; b, tripartite song of R. r. azoricus, São Miguel; syntax: introduction (unit 1) + mid part (ascending phrase, unit 2) + final part (terminal flourish, unit 3); c, parameters measured in sonagraphic analysis indicated by horizontal and vertical lines; d, subsong of R. r. japonensis, Far East Siberia; from a continuous performance of about two minutes.
FIGURE 3 in Song dialects as diagnostic characters - acoustic differentiation of the Canary Island Goldcrest subspecies Regulus regulus teneriffae Seebohm 1883 and R. r. ellenthalerae Päckert et al. 2006 (Aves: Passeriformes: Regulidae)
FIGURE 3. Scatterplot of discriminant function 1 vs. function 2 for subunits of main song part of Canarian Goldcrest dialects and for subsong trills.
FIGURES 5a–o in Song dialects as diagnostic characters - acoustic differentiation of the Canary Island Goldcrest subspecies Regulus regulus teneriffae Seebohm 1883 and R. r. ellenthalerae Päckert et al. 2006 (Aves: Passeriformes: Regulidae)
FIGURES 5a–o. Territorial song of Regulus regulus ellenthalerae, song types indicated on the sonagrams, lower left. El Hierro: a–b, song type A2 with interposed element (arrows) between units 1 and 2, two different males; c–g, song type E with two local rhythmic motifs of unit 2, three different males; h) variation of type A with calllike elements; La Palma: i–o, song type F with more or less extended ascending unit 2 consisting of diverse modulated element types, five different males (i, k: two strophes of one male).
R code of the mechanism controlling soil bacterial α and β diversity under N addition
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FIGURE 6. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 6. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R. nasuta, based on 3620 bp of nuclear DNA (partial Rag 1, Rag 2, C-mos, R35 and ODC genes). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities> 0.95 in Bayesian analyses. Note the monophyly of R. melanosterna; lineages I–IV are distributed in the western part, lineages VI and VII in the eastern part of the range.
FIGURE 5. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 5. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R. nasuta, based on 2050 bp of mitochondrial DNA (partial cyt b, 12S and 16S genes). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities of 1.0 in Bayesian analyses (no other branches had support values equal to or greater than 0.95). Note the polyphyly of R. melanosterna.
FIGURE 7. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 7. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R. nasuta, based on the supermatrix of 2050 bp of mitochondrial DNA (partial cyt b, 12S and 16S genes) concatenated with 3620 bp of nuclear DNA (partial Rag 1, Rag 2, C-mos, R35 and ODC genes). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities of 1.0 in Bayesian analyses (no other branches had support values equal to or greater than 0.95; for further explanation see text). Root length shortened by 80%. Note the weak support for the monophyly of R. melanosterna and most other clades.
FIGURE 4 r in Revision of the Southern African leafhopper genus Pravistylus (Hemiptera, Cicadellidae, Deltocephalinae) 2468
FIGURE 4 r–ai. Pravistylus species. Aedeagus, dorsally or ventrally. r–t, P. pollediscus sp. n., dorsal; u, P. scolopygeus sp. n., ventral; v, P. dentidiscus sp. n., ventral; w, P. micropygeus sp. n., dorsal; x, P. trunculidiscus sp. n., dorsal; y, P. interdiscus sp. n., dorsal; z, P. longitrunculus sp. n., dorsal; aa, P. oxyphysis sp. n., dorsal; ab, P. digitidiscus sp. n., dorsal; ac, P. serratus sp. n., dorsal; ad, P. indistinctidiscus sp. n., dorsal; ae, P. varicudiscus sp. n., dorsal; af, P. odontopygeus sp. n., dorsal; ag, P. pelorophallus sp. n., dorsal; ah, P. scolophallus sp. n., ventral; ai, P. caenophallus sp. n., ventral.
Figs. 2–5. Cybocephalus flavocapitis T. R. Smith, new species. 2 in Figs. 30– 33. Attavicinus monstrosus. 30 in Comparison of Mouthpart Morphology of Three Species of Mexican Oniticellini (Coleoptera: Scarabaeidae: Scarabaeinae) in Relation to Their Trophic Habits
Figs. 2–5. Cybocephalus flavocapitis T. R. Smith, new species. 2) antenna; 3) median lobe, dorsal view; 4) median lobe, lateral view; 5) basal plate, ventral view.
NextClone and CloneDetective: An Integrated Nextflow Pipeline and R Package for Clonal Barcode Extraction and Quantification
<p>BAM file (chunk 26-50 of 50) for the scRNAseq data required to replicate the analyses presented at: https://phipsonlab.github.io/NextClone-analysis/.</p><p>Chunk 1-25 can be downloaded from https://zenodo.org/records/10129134.</p><p>The original BAM file was too big to fit in an entry. Thus it was split into 50 using picard:</p><blockquote><p>SplitSamByNumberOfReads -I possorted_genome_bam.bam -O split_sam/ -N_FILES 50 <i>--CREATE_MD5_FILE</i></p></blockquote><p>Before re-running all the analyses in https://phipsonlab.github.io/NextClone-analysis/, make sure you merge all 50 chunks first using picard (change xxx to point to the directory storing all the 50 chunks you have downloaded):</p><blockquote><p>outdir="xxx"</p><p>args=""</p><p><i># Loop through each BAM file</i></p><p>for file in ${outdir}/*.bam; do</p><p> args+="-I $file "</p><p>done</p><p># Do the actual merging</p><p>MergeSamFiles $args -O $outdir/merged_v2/merged_bam_v2.bam --USE_THREADING --CREATE_MD5_FILE</p></blockquote><p>Picard can be downloaded from: https://github.com/broadinstitute/picard</p>
NextClone and CloneDetective: An Integrated Nextflow Pipeline and R Package for Clonal Barcode Extraction and Quantification
<p>BAM file (chunk 1-25 of 50) for the scRNAseq data required to replicate the analyses presented at: https://phipsonlab.github.io/NextClone-analysis/.</p><p>Chunk 26-50 can be downloaded from https://zenodo.org/uploads/10129625</p><p>The original BAM file was too big to fit in an entry. Thus it was split into 50 using picard:</p><blockquote><p>SplitSamByNumberOfReads -I possorted_genome_bam.bam -O split_sam/ -N_FILES 50 <i>--CREATE_MD5_FILE</i></p></blockquote><p>Before re-running all the analyses in https://phipsonlab.github.io/NextClone-analysis/, make sure you merge all 50 chunks first using picard (change xxx to point to the directory storing all the 50 chunks you have downloaded):</p><blockquote><p>outdir="xxx"</p><p>args=""</p><p><i># Loop through each BAM file</i></p><p>for file in ${outdir}/*.bam; do</p><p> args+="-I $file "</p><p>done</p><p># Do the actual merging</p><p>MergeSamFiles $args -O $outdir/merged_v2/merged_bam_v2.bam --USE_THREADING --CREATE_MD5_FILE</p></blockquote><p>Picard can be downloaded from: https://github.com/broadinstitute/picard</p>
FIGURE 4. R in Rohdea brachyanthera (Asparagaceae), a new species from Guangdong, southern China
FIGURE 4. R. watanabei in Hunan population. A. Habit. B. Inflorescence. C. Bracts. D. Flower, lateral view. E & F. Flower, vertical view. G & I. Flower, longitudinal section. H. Flower, vertical view and perianth tube had been cut open. Cultivated in nursery of Zaozhuang University, Shandong, China.
FIGURE 1. Rubus fairholmianus Gardner. A in Taxonomic delineation of two closely allied Rubus L. (Rosaceae) species with notes on the typification of the name R. fairholmianus
FIGURE 1. Rubus fairholmianus Gardner. A. Habitat; B. Inflorescence (showing abaxial surface of leaves); C. Flower; D. Fruit; E. Stem (showing glaucous); F. Prickle; G. Adaxial surface of stipule; H & I. Sepals (showing adaxial and abaxial surface respectively); J. Petal; K. Adaxial surface of bract; L. Stamens; M. Carpels; N. Drupelets. (Photos: Bhavadas N and Saleesh J Menachery).
FIGURE 3. Rubus micropetalus Gardner. A in Taxonomic delineation of two closely allied Rubus L. (Rosaceae) species with notes on the typification of the name R. fairholmianus
FIGURE 3. Rubus micropetalus Gardner. A. Habitat; B. Inflorescence; C. Abaxial surface of leaves; D. Flower; E. Fruits; F & G. Stipules (showing adaxial and abaxial surface); H & I. Sepals (showing adaxial and abaxial surface); J. Petal; K & L. Bracts (showing adaxial and abaxial surface); M. Drupelet. (Photos: Bhavadas N).
ScienceDex guides
Understand access before you commit
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.