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Figure 7 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 7. Simultaneous diversification (splitting events) through time in crocodile newts (blue bars) and the similarly surveyed South-East/East Asian tree frog genus Zhangixalus (green bars; Dufresnes et al., 2022), overlaid by Earth temperature (red curve). The latter is shown as the difference with the average temperature over the 1960–90 period, combining the datasets from Zachos et al. (2008), Hansen et al. (2013) and Lisiecki & Raymo (2005). In both amphibians, ancestral clades diverged in the Early Miocene and probably expanded throughout Asia during the Miocene climatic optimum; extant clades and species then appeared as the climate progressively cooled down and the South-East Asian monsoon strengthened in the Late Miocene onwards, and recently accelerated during the Pleistocene Quaternary glaciations. Photos: E. maxiquadratus (credit: AH) and Z. chenfui (credit: S. N. Litvinchuk).
Figure 8 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 8. Portrays of subgenera Sinotriton subgen. nov. and Echinotriton. Notice the shape of the vertebral ridge (segmented in Sinotriton vs. smooth in Echinotriton) and the fifth toe (normally developed in Sinotriton vs. rudimentary in Echinotriton). Photos: E. chinhaiensis, E. maxiquadratus (credits: AH); E. andersoni, E. raffaellii (credits: J. Nerz).
Inversion polymorphism in a complete human genome assembly
<p>Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.</p>
FIGURE 3. Correlation between the genetic p in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 3. Correlation between the genetic p-distances of the barcoding region (cox1) and the 13PCGs of the E. nordenskioldi s.l. taxa.
FIGURE 2 in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 2. Phylogenetic relationships of 14 Lumbricidae species, based on the nucleotide sequences of the 13 PCGs. Drawida japonica was included as an outgroup. Numbers at the branches represent Bayesian probabilities and bootstrap support (%). The blue clades represent unpigmented, the red ones pigmented specimens. The two unpigmented Korean specimens are marked in malachite-green.
FIGURE 1 in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 1. Phylogenetic relationships of 33 Crassiclitellata species, including E. nordenskioldi cf. pallida No. 1 and No. 3, based on the 13 PCG nucleotide sequences. Drawida japonica was included as an outgroup. Numbers at the branches represent ML bootstrap support.
Phylogenetic Analysis Based on the Complete Mitochondrial Genomes of Eight Nymphalidae Species (Lepi-doptera: Papilionoidea)
<p>Table S1: Basic sequence characteristics of mitochondrial genomes of eight newly sequenced species in Nymphalidae;</p> <p>Table S2: Base composition, AT content, AT-skew, GC-skew and total length (bp) of 105 species in all three codon positions, codon position 1, codon position 2 and codon position 3 in this study. The species highlighted in red are the ones that were sequenced;</p> <p>Table S3:<strong> </strong>Taxonomic information and GenBank accession numbers for 105 mitogenomes in Nymphalidae selected for characteristics and phylogenetic analysis in this study.</p>
Duplo: Complete Task
<p>This video shows what the complete task looks like in the Duplo experiment. Its important to emphasize that participants didn't have to follow the same assembly order.</p>
A complete list of filtered variants and gene lists of frequently and recurrently mutated genes in 25 MCL patients at diagnosis compared to relapse, as well as a CNV genelist
<p>Supplemental Table 1 shows a complete list of variants which passed filtering described in supplemental methods, that were found in both diagnostic samples and relapsed samples (i.e., shared variants, sheet 1A), variants that were newly detected – N/D (sheet 1B) or newly undetected – N/U (sheet 1C). Gene lists for filtration of variants and CNV changes in genes of special interest are included in the table (sheet 1D). Chr - Chromosome, REF - Reference allele, ALT - Alternative allele, AA change - Amino acid change, DG_AF – Variant Allele frequency in the diagnostic sample, DG_Depth - Read depth in the diagnostic sample, REL_AF - Variant Allele frequency in the relapsed sample, REL_Depth - Read depth in the relapsed sample, SNV - Single Nucleotide Variant, and CNV - Copy Number Variation. </p>
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
<span>Background</span> <p><em><span>Abies koreana</span></em><span> E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history.</span></p> <span>Results</span> <p><span>Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from <em>A. koreana</em>. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of <em>A. koreana</em>. The short inverted repeats (1,186 bp) of the <em>A. koreana</em> plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using <em>A. koreana</em> as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (<em>Balsamea</em>, <em>Momi</em>, and <em>Pseudopicea</em>) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization.</span></p> <span>Conclusions</span> <p><span>These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within <em>Abies</em> and new insights into the phylogenomic complexity of this genus.</span></p>
MOON: Assisting Students in Completing Educational Notebook Scenarios (Artifacts)
<p>This repository contains the artifacts supporting the paper "<em>MOON: Assisting Students in Completing Educational Notebook Scenarios</em>" published in the <em>IEEE Symposium on Visual Languages and Human-Centric Computing</em> (VL/HCC) 2023.</p> <ul> <li><strong>moon.zip</strong> contains the source code of MOON at the time of publication</li> <li><strong>notebooks.zip</strong> contains the example Jupyter notebook used as illustration in the paper as well as the notebook manipulated by students in the evaluation</li> <li><strong>analysis.zip</strong> contains the Jupyter notebooks used to analyze the raw data extracted in the evaluation as well as the results of the user study conducted with students</li> </ul>
complete_allsides_data
<p>complete allsides newsarticle data</p>
complete_allsides_data_cleaned
<p>cleaned complete allsides data, without citations and special characters in the fulltexts</p>
FIGURE 3 in Taxonomy and nomenclature of Kalanchoe tomentosa (Crassulaceae subfam. Kalanchooideae), a variable, completely hairy species from Madagascar
FIGURE 3. Epitype, [R.] Baron 3560, K K000232863 [http://specimens.kew.org/herbarium/K000232863], designated in this paper, in support of the holotype of the name Kalanchoe tomentosa. "Central Madagascar. Received Nov. 1885." Reproduced with the kind permission of the Director and the Board of Trustees, Royal Botanic Gardens, Kew.
FIGURE 2 in Taxonomy and nomenclature of Kalanchoe tomentosa (Crassulaceae subfam. Kalanchooideae), a variable, completely hairy species from Madagascar
FIGURE 2. Holotype, [R.] Baron 247, K K001040417 [http://specimens.kew.org/herbarium/K001040417; not yet available online], of the name Kalanchoe tomentosa. "Central Madagascar, chiefly in Betsileo-land, recd. July 1880, [R.] Baron 247. Reproduced with the kind permission of the Director and the Board of Trustees, Royal Botanic Gardens, Kew.
FIGURE 1. A in Taxonomy and nomenclature of Kalanchoe tomentosa (Crassulaceae subfam. Kalanchooideae), a variable, completely hairy species from Madagascar
FIGURE 1. A. Portrait of John Gilbert Baker (1834–1920) who published the name Kalanchoe tomentosa in 1882. Reproduced from Journal of Botany, British and Foreign. London, volume 39 (1901). Photograph: Berthold Carl Seemann. Public Domain. http://www.plantillustrations.org/illustration.php?id_illustration=176522. B. Portrait of Reverend Richard Baron (1847–1907) who collected the material on which Baker based the name K. tomentosa. Credit of the photograph is to Fiangonan' I Jesoa Kristy Eto Madagasikara (FJKM), which is the lineal descendent of the London Missionary Society, Antananarivo, which employed Baron. Permission was granted to Dr Laurence J. Dorr by FJKM to disassemble a framed collection of photographs of 19th century missionaries to obtain individual portraits for use in Dorr (1997). Dr Dorr kindly supplied the image to the author of this paper. C. Kalanchoe tomentosa is a sparsely- to many-leaved, entirely hairy, sparsely branched, small to medium-sized, terrestrial, succulent shrub that can reach a height of about 1 m. Note the hard, stiff aerial roots that often develop on the stem and branches. D. The hairy flowers of K. tomentosa are borne erect to erectly spreading to spreading, and are hairy throughout. Flowers are campanulate to sometimes very slightly urceolate, yellowish brown to greenish and often sometimes purple-infused. The corolla lobes are light to deep purple on a greenish background, and adaxially velvety rather than hairy. Photographs C and D taken by Gideon F. Smith.
Figure 5. Scolelepis juvenile and adult morphology. A, complete 40 in Origin of the pointed snout in Scolelepis and the mouth region in spionid polychaetes (Annelida: Spionidae)
Figure 5. Scolelepis juvenile and adult morphology. A, complete 40-chaetiger juvenile, leħ lateral view. B, anterior end of a 60-chaetiger adult, frontal view. C, D, F, anterior ends, dorsal view. E, palps of the specimen shown on B. G, anterior end, leħ lateral view, leħ palp missing. Abbreviations: la, ciliated lateral organ; lp, lateral peristomial lip; nt, nototroch; nu, nuchal organ; pa, palp scar; pp, pointed peristomial process; sh, basal sheath on palp; s1, s2, segments 1, 2; arrow shows boundary between the pointed peristomial process and the prostomium. Scale bars: A, 200 µm; B–D, F, G, 100 µm; E, 50 µm. A, B, E, S. goodbodyi, São Sebastião, São Paulo, Brazil (MZUSP 251). C, Scolelepis sp. A, Paranaguá Bay, Paraná, Brazil. D, Scolelepis sp. B, Peter the Great Bay, Sea of Japan, Russia (MIMB). F, G, Scolelepis sp. C, Peter the Great Bay, Sea of Japan, Russia (MIMB).
Haplotype variations data for the complete 5.3 Mbp region
<p><em>Variations </em>data for the complete chromosome 2A 5.3 Mbp region +/- 1 Mbp of the whole dataset.</p>
Supplementary video of Petrini et al. 2023, submitted to TC. "Topographically-controlled tipping point for complete Greenland Ice Sheet melt"
<p>Animations showing the evolution of the Greenland Ice Sheet in simulations with different SMB and global mean temperature levels. </p>
CityLoops - Circular economy indicator set (complete)
<p>This file contains a list of 446 circular economy (CE) indicators compiled by Nordland Research Institute from an extensive review of the CE monitoring framework literature, carried out as part of the Horizon 2020 project CityLoops (GA no. 821033). Frameworks and indicators with relevance for a European city setting were prioritized for inclusion on the list. In the dataset, each indicator is presented with a brief definition and a literature reference and classified along various dimensions to facilitate filtering of the data. The dataset was compiled during the period 2019-2020. Expired hyperlinks were updated in September 2023.</p>
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.