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1,254 results for “PANs”
FIGURES 8–19 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURES 8–19. Median lobe of aedeagus in ventral and lateral view: 8) Paroster michaelseni (holotype), 9) P. baylyi sp. n., 10) P. u r s u l a e sp. n.; Left paramere: 11) P. michaelseni (holotype), 12) P. baylyi sp. n., 13) P. u r s u l a e sp. n.; Gonocoxae: 14) P. michaelseni, 15) P. baylyi sp. n., 16) P. u r s u l a e sp. n.; Gonocoxosternum: 17) P. michaelseni, 18) P. baylyi sp. n., 19) P. u r s u l a e sp. n.
FIGURES 23–28 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURES 23–28. Habitats of Paroster baylyi sp. n. and P. ursulae sp. n., various pan-gnammas: 23) Type locality of P. ursulae sp. n., granite outcrop 80 km WSW Coolgardie {10}; 24) Stephan Gottwald searching for P. ursulae sp. n. {10}; 25) Type localities of P. baylyi sp. n., "Bilya Rock", 25 km ENE Morawa {1}; 26, 27) "Camel Soak", 31 km E Perenjori {2}; 28) "Rockpools", 10 km E Wubin {3}.
FIGURE 9 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 9. (A), (B) and (C) Dorsolateral color pattern of three specimens of Allobates femoralis photographed near Barranquita (6.2653°S, 76.0434°W), 36 km from Allobates femoralis type locality in Yurimaguas, Loreto, Peru. (D) Ventral view of same individual B, showing exclusively black and white color patterning on belly and ventral surface of thighs. Photos are courtesy of Jason L. Brown.
FIGURE 7 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 7. Maximum Likelihood phylogenetic tree reconstructed from unique haplotypes of a 518 b.p. fragment of the mitochondrial gene 16S rRNA of Allobates femoralis and Allobates hodli sp. nov. sampled in 13 localities in Brazilian Amazon. Data set included reference sequences from Peru, Colombia, Ecuador, Suriname and other localities in Brazil obtained from GenBank. (A) Phylogenetic position of the clade including A. hodli sp. nov. and A. femoralis in relation to outgroups supports Allobates zaparo as their sister group. Clade labels represent support values from 5000 bootstrap replicates (only values above 50 are shown). (B) Relative phylogenetic placement of clades within the ingroup. Sample oscillograms and sonograms of advertisement calls from populations within clades display natural variation in number of notes. A. hodli is closely related to populations of A. femoralis from the southern Brazilian state of Acre (clade Acre 01), which present a four-note advertisement call and color pattern characteristic of A. femoralis. Both form the sister group to samples from northwestern Acre and from the Madre de Dios River basin (clade Acre 02). The basal clade containing A. hodli and Acre 01 and Acre 02 clades is the sister group to a basal clade containing A. femoralis sensu stricto (placed in the weakly supported clade femo 04) and the other reference sequences from populations referred to as A. femoralis (clades femo 01, femo 02, femo 03, femo 04). Samples from Ecuador form a divergent and well supported clade, with advertisement calls formed by a single note. Individuals from Panguana (placed in clade femo 04) present a distinctive 3- note advertisement call (not shown). All remaining populations have advertisement calls constituted by four notes. Calls from Yasuní, Ecuador, published by Read (2000). Calls from Pongo de Cainarachi, Peru (about 45 km south from A. femoralis type-locality in Yurimaguas) provided by Jason L. Brown. (C) Corresponding values on axes of oscillograms and sonograms of advertisement call samples.
FIGURE 8 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 8. Advertisement calls of Allobates femoralis recorded in (A) Chazuta (6.5419°S, 76.1083°W) and (B) Pongo de Cainarachi (6.2974°S, 76.2343°W), both localities in San Martin, south of A. femoralis type-locality in Yurimaguas. In both sites, calls are constituted by groups of four frequency-modulated notes. Sounds appearing with peak frequency at approximately 4.0 kHz in B are background noise. Recordings are courtesy of Jason L. Brown.
FIGURE 6 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 6. The advertisement calls of Allobates hodli are constituted by trills of two notes repeated in series. (A) Waveform and sonogram of advertisement calls of A. hodli holotype (INPA–H 16555) recorded at Cachoeira do Jirau, Rondônia, at 07:55 h., in November 2004, air temperature 25.3°C, scaled to evidence ascending frequency modulation of notes. (B) Advertisement call of holotype in a larger scale, evidencing continuous repetition of two-note calls. (C) Advertisement call of an A. hodli male paratype (SVL = 24.62 mm) from Abunã, Rondônia, recorded at 24.7°C. (D) Courtship call of one A. hodli male (INPA-H 16553, SVL = 23.84 mm) recorded at type locality at 09:00 h, in November 2004, air temperature 26.3°C.
FIGURE 3 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 3. (A) Dorsal and (B) ventral views of Allobates hodli holotype (INPA-H 16555), a male collected at Cachoeira do Jirau in November, 2004. This individual lacks the disgestive tract and liver, removed for diet and genetic analyses respectively. (C) and (D) Hand and foot of A. hodli holotype.
FIGURE 2 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 2. Color in life of Allobates hodli sp. nov. (A) Lateral view of and adult male from Abunã, in Rondônia. (B) Dorsal view of a male from Cachoeira do Jirau, Rondônia. (C) Ventral view of an adult male from Fazenda Catuaba, in Acre, photographed through a transparent plastic bag. Note bright reddish–orange color of posterior abdomen and ventral surface of legs. (D) Ventral view of a male (left) and a female (right) from Cachoeira do Jirau. (E) Dorsolateral view of a male from Cachoeira do Jirau. Note irregular reddish-orange and black blotches and spots on dorsal surface of thighs and bright yellow flash marks on upper arms. (E) Juvenile from Abunã, photographed in laboratory after completion of metamorphosis. Photos A–C taken under natural light conditions. Photos A, B, D and E taken in July 2004; C in January 2003; A–E by Walter Hödl. F taken in February 2005 by A.P. Lima.
FIGURE 1 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 1. Relative location and denomination of (A) sampling sites in the Brazilian States of Acre and Rondônia, and (B) sampling sites and locations from where Allobates femoralis 16S rRNA mtDNA reference sequences were available in the Amazon Basin (shaded in paler gray). Yellow dots represent the distribution of Allobates hodli sp. nov. Lightgreen, dark-green, and black dots represent localities of samples referred to as A. femoralis, including two sites (5 and 9) where A. hodli reaches contact zones with these populations. Dot colors stand for major lineages recovered by phylogenetic analysis of a partial sequence of the 16S rRNA mitochondrial gene (see text and Fig. 7). Site 20, Yurimaguas, is considered the closest to A. femoralis type locality.
FIGURE 4 in The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)
FIGURE 4. (A) Dorsal view of preserved Allobates hodli tadpole in developmental stage 36 collected at Abunã, on the left bank of the upper Madeira River, in Rondônia, Brazil, on January 2005 (INPA-H 23693). (B) and (C) Ventral and lateral views of the same tadpole, respectively.
Supplemental tables for 'Pan-microalgal dark proteome mapping via interpretable deep learning and synthetic chimeras'
<p>Distinguishing genuine microbial proteins from contaminants remains a major bottleneck in genomics, particularly for environmental and non-model organisms where conventional homology-based tools are slow, resource-intensive, and leave large fractions of the "dark proteome" unclassified. LA<sup>4</sup>SR offers a scalable, interpretable framework that classifies algal and bacterial proteins directly from translated sequence data, achieving near-complete recall while accelerating inference by ~ 10,000-fold relative to BLASTP. By revealing that internal sequence features alone can drive robust classification, LA4SR bypasses the need for complete gene models or perfect annotations—opening new opportunities for analyzing complex microbial communities and metagenomes. Interpretability methods further link emergent amino acid signatures to evolutionary and ecological features, highlighting the potential of language models not only to accelerate genomics workflows but also to uncover new biological insights.</p> <p> </p> <p><strong>Table S1 | External spreadsheet. </strong>This spreadsheet contains LA<sup>4</sup>SR performance metrics, technical performance estimations, and BLAST results and runtimes of genomes comprising the algal training data.<strong> </strong></p> <p><strong>Table S2 | External spreadsheet. </strong>Captum attributions for 100 sequences each of algal and bacterial origin obtained using the LayerIntegratedGradients function.</p> <p><strong>Table S3 | External spreadsheet. </strong>Influential motifs found with the DeepMotifMinerPro software introduced in this work (see Data S3).</p> <p><strong>Table S4 | External spreadsheet.</strong> LA4SR and Diamond BLAST results for data from new assemblies from seen species (Fig. S7), contaminated assemblies from unseen genera (Fig. S7), and clean assemblies from unseen genera (Fig. 8). For the LA4SR results for genome assemblies from unseen genera, the genomes were published after the model was trained, and the genera shown were not included in the training dataset. Newly sequenced genomes uploaded to NCBI SRA accession SUB14799921.</p> <p> </p> <p> </p>
Updated Metagenomic Species Pan-genomes (MSPs) of the human gastrointestinal microbiota
<p></p><h1>Gene catalog construction</h1><br>The methodology for creating the IGC2 catalog is described in the original papers: Li et al., 2014 and Wen et al., 2017<br><h1>MSP creation</h1><br>Reads from publicly available human gut metagenomes were aligned against the IGC2 catalog with the Meteor to produce a raw gene abundance table (10.4M genes quantified in >2000 samples). Then, co-abundant genes were binned in 1,989 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.<br><h1>MSPs taxonomic annotation</h1><br>MSPs taxonomic annotation was performed by aligning MSP core and accessory genes against representative genomes of the Genome Taxonomy Database (GTDB r207) using blastn (task = megablast, word_size = 16). The 20 best hits for each gene were kept (--max-target-seq 20). Using an in-house pipeline, a species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.<br><h1>Construction of the phylogenetic tree</h1><br>39 universal phylogenetic markers genes were extracted from the MSPs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni). <h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB1786, PRJEB5224, PRJEB6337, PRJNA422434 (cohort used in catalogue assembly) and PRJEB11532, PRJEB33500, PRJEB37249, PRNJNA834801 (independent cohort not used in assembly).<p></p>
Fig. 3. Enema pan adult and larva. a in Observations on the Life History ofEnema pan(F.) (Coleoptera: Scarabaeidae: Dynastinae) and Its Association with Bamboo,GuaduaKunth (Poaceae: Bambusoideae), in Southwestern Amazonia
Fig. 3. Enema pan adult and larva. a) Male inside mound, b) Male perching on top of mound, c) Larva (inset) collected inside burrow along with wet, crushed leaves and sticks (main image), d) Male near burrow after excavation of burrow; this individual was found at the end of the main tunnel after excavation.
Fig. 1 in Observations on the Life History ofEnema pan(F.) (Coleoptera: Scarabaeidae: Dynastinae) and Its Association with Bamboo,GuaduaKunth (Poaceae: Bambusoideae), in Southwestern Amazonia
Fig. 1. Sketches of the burrow structure made by Enema pan. a) Profile view of entire burrow with offshoots; in this burrow, the end of the main tunnel was approximately 1 m underground, b) Close-up view of the top of the burrow, mound, and shredded portion of bamboo. The top of the mound (hatched marks) illustrates the portion of the soil that is removed at night when the beetle emerges and perches on the top of the mound.
Fig. 2 in Observations on the Life History ofEnema pan(F.) (Coleoptera: Scarabaeidae: Dynastinae) and Its Association with Bamboo,GuaduaKunth (Poaceae: Bambusoideae), in Southwestern Amazonia
Fig. 2. Photographs illustrating the mound and burrow of Enema pan at the base of a bamboo stem. a) The mound at the base of a bamboo stem, b) Excavation of the mound, c) An excavated mound with a Swiss army knife (9 cm length) for perspective, d) The same excavated mound with pieces of pink flagging to illustrate the path of the underground portion of the burrow.
Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
<p><span>Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ~40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (>46.5X) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchored in a gene body or regulatory region are linked to domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression of <em>IGF2BP1</em> and generate novel transcripts of <em>MITF</em>, shaping body weight and plumage color. In the <em>IGF2BP1</em> locus, the TE-derived SV explains the largest effect on body weight among avian species (27.61% of phenotypic variation). Our findings highlight the </span><span>importance of using a pan-genome as a reference in genomics studies</span><span> and explore the roles of TE-derived SVs in trait formation and in livestock breeding.</span></p>
Datasets for the study "A Pan-Cancer Single Cell Panorama of Human Natural Killer Cells"
<p>File "comb_CD56_CD16_NK.h5ad" contains processed expression data and raw count data used in most part of the paper and annotations such as "meta_tissue_in_paper" and "cellType".</p><p>File "comb_CD56_CD16_NK_blood.h5ad" contains processed expression data used in the analysis of circulating NK cells and annotations such as "meta_tissue" and "cellType".</p><p>File "Integrated_CD16_NK cells.h5ad" contains processed expression data of CD56dimCD16hi NK cells used in most part of the paper and annotations such as "meta_tissue_in_paper" and "cellType".</p><p>File "Integrated_CD56_NK cells.h5ad" contains processed expression data of CD56brightCD16lo NK cells used in most part of the paper and annotations such as "meta_tissue_in_paper" and "cellType".</p>
Cycladic Frying Pan Draft
Model being developed as part of the #[CEEF3D](https://creative-economy.fitzmuseum.cam.ac.uk/) Being An Islander [Museum in a Box](http://creative-economy.fitzmuseum.cam.ac.uk/projects/project-four-miab-mediterranean/) project. More information on the object can be found here: https://webapps.fitzmuseum.cam.ac.uk/explorer/index.php?oid=69695 Source: Objaverse 1.0 / Sketchfab
Pan Poursuivant Syrinx - Cap Re
Pan pursuing Syrinx (1804), Gilles-Lambert Godecharle (1750-1835). Royal Museums of Fine Arts of Belgium (Brussels, Belgium). Made with CapturingReality. For more updates, please consider to follow me on Twitter at @GeoffreyMarchal. Source: Objaverse 1.0 / Sketchfab
Data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA"
<p>This submission has processed data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA".</p> <p>The `data` folder contains processed information for the Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) datasets. The HPA data is found in `data/hpa` and contains gene ranks used to compute the thymus-likeness score (TLS) and files where the TLS has been calculated for the HPA tissues. The TCGA data can be found in `data/proc`, where individual RDS files have been given for each analyzed cohort. These RDS files contain the results of the cutoff scanning procedure mentioned in the manuscript and account for the bulk of the data generated for this study. RDS files can be loaded using the `readRDS` function in an R session. Other information used to create plots is in the `data` folder.</p> <p>The `plots` folder contain the result of plotting the entireity of the cutoff scanning procedure. The manuscript only contains plots for the 28 cohorts where a significant difference in terms of immune difference is observed, and that too, only the final heuristic plots. The `plots/tcga/immuneres` folder has plots at different levels: (i) single cell category/single deconvolution method with permutation tests (ii) single cell category/multiple deconvolution methods and (iii) significant cell categories/representative deconvolution method. Only (iii) is present in the manuscript. Overall, this folder should contain ~2000 plots.</p> <p>The code used to generate this study is deposited at: https://gitlab.com/narencs179/thymus-like-score</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.