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1,019 results for “Assignment”
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem
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FIGURES 71–73. Phyllonorycter tritaenianella. 71 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 71–73. Phyllonorycter tritaenianella. 71: Early leaf mine on Ostrya virginiana (larvae feeding right of center); 72: Reared adult; 73: Mature leaf mine.
FIGURES 30–32. Phyllonorycter celtisella. 30 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 30–32. Phyllonorycter celtisella. 30: Lower surface of leaf mine on Celtis occidentalis (note short initial portion formed on lower surface at upper right); 31: Upper surface of the same mine (note longitudinal crease in blotch portion, with protruding pupal exuviae); 32: Reared adult.
FIGURES 1–4. Anarsioses aberrans. 1 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 1–4. Anarsioses aberrans. 1: Mines of four larvae in a leaf of Desmodium perplexum; 2: Coalescing mines of four larvae in a leaflet of Lespedeza hirta; 3: Spread adult; 4: Adult reared from D. perplexum.
FIGURES 35–37. Phyllonorycter holodisci. 35 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 35–37. Phyllonorycter holodisci. 35: Flat, aborted, upper-surface leaf mine on Holodiscus discolor; 36: Tentiform, more advanced mine; 37: Holotype, reared by A.F. Braun (photo: J.D. Weintraub/ANSP Entomology).
FIGURES 68–70. Phyllonorycter tiliacella. 68 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 68–70. Phyllonorycter tiliacella. 68: Occupied leaf mine on Tilia americana; 69: Vacated mine with pupal exuviae protruding at right; 70: Reared adult.
FIGURES 53–55. Phyllonorycter mariaeella. 53 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 53–55. Phyllonorycter mariaeella. 53: Leaf mine on Lonicera japonica (upper surface); 54: Lower surface of the same mine, with pupal exuviae protruding at far right; 55: Mine on L. japonica with lower epidermis torn open to show frass (left) and cocoon (center).
FIGURES 27–29 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 27–29. Phyllonorycter argentinotella reared from an underside tentiform mine on Ulmus sp. in Iowa. 27: Upper surface of mine; 28: Lower surface; 29: Adult.
FIGURES 43–44. Phyllonorycter leucothorax adults. 43 in Wrong side of the leaf: assigning some Lithocolletinae species (Lepidoptera: Gracillariidae) to their proper genera
FIGURES 43–44. Phyllonorycter leucothorax adults. 43: Wings and habitus; 44: Head and forewing illustration.
Figs. 7–15 in Dyticodopoea And Pygmaeodopoea, New Genera For The Central American Cicada Species Previously Assigned To Odopoea Stål, 1861 (Hemiptera: Cicadoidea: Cicadidae: Cicadinae: Zammarini)
Figs. 7–15. Comparison of Dyticodopoea Sanborn, n. genus, Pygmaeodopoea Sanborn, n. genus and Odopoea Stål, 1861 male genitalia and timbal covers. 7, Dyticodopoea signoreti (Stål, 1864) new combination lateral view of male genitalia. Scale bar = 1 mm. 8, Dyticodopoea signoreti (Stål, 1864) new combination posterior view of male genitalia. Scale bar = 1 mm. 9, Dyticodopoea signoreti (Stål, 1864) new combination timbal cover. Scale bar = 2 mm. 10, Pygmaeodopoea minuta (Sanborn, 2007) new combination lateral view of male genitalia. Scale bar = 1 mm. 11, Pygmaeodopoea minuta (Sanborn, 2007) new combination posterior view of male genitalia. Scale bar = 1 mm. 12, Pygmaeodopoea minuta (Sanborn, 2007) new combination timbal cover. Scale bar = 2 mm. 13, Odopoea strigipennis (Walker, 1858) lateral view of male genitalia. Scale bar = 1 mm. 14, Odopoea funestra (Walker, 1858) posterior view of male genitalia. Scale bar = 1 mm. 15, Odopoea dilatata (Fabricius, 1775) timbal cover. Scale bar = 2 mm.
MCMC data for A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection
<p>These are unprocessed Markov-chain Monte-Carlo datasets accompanying the manuscript "A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection"</p>
IO Islamic 1017. Majma'-alḥasanât, A Second Work to Which the Title of قصص الانبیا is Assigned
<p>IO Islamic 1017. Majma’-alḥasanât, A Second Work to Which the Title of قصص الانبیا is Assigned</p>
IO Islamic 3489. Majma'-alḥasanât, A Second Work to Which the Title of قصص الانبیا is Assigned
<p>IO Islamic 3489. Majma’-alḥasanât, A Second Work to Which the Title of قصص الانبیا is Assigned</p>
FIGURE 5. Pseudopanopeus pusillus n. comb. A in A new crab of the genus Nanoplax from the Gulf of Mexico, and assignment of Micropanope pusilla to a new genus (Crustacea, Brachyura, Pseudorhombilidae)
FIGURE 5. Pseudopanopeus pusillus n. comb. A, male, cw 5.7 mm (ULLZ 8058 = USNM 1536348) northeastern Gulf of Mexico; B, male, cw 5.6 mm (ULLZ 14362 = USNM 1536353) northeastern Gulf of Mexico; C, male, cw 5.2 mm (ULLZ 2388 = USNM 1536336) northeastern Gulf of Mexico; D, male, cw 5.2 mm (ULLZ 14362 = USNM 1536353) northeastern Gulf of Mexico; E, male, cw 5.0 mm (ULLZ 6776 = USNM 1536339) southwestern Gulf of Mexico.
Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples
Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We demonstrate that both blunt-ending and post-ligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.
Assigning the sex-specific markers via genotyping-by-sequencing onto the Y chromosome for a torrent frog Amolops mantzorum
<p><span>We use a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (<i>Amolops mantzorum</i>) using wild-caught individuals of 21 males and 19 females from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS tags through three approaches, respectively based on sex differences in allele frequencies, sex difference in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope, amplified by whole-genome amplification, and assembled a draft Y genome. 55 out of 69 sex-linked markers could be mapped to the Y chromosome assembly (i.e 79.7 %). Thus the chromosome 5 could be added as candidate chromosomes that particularly favored to recruit for sex determination than others among frogs. Three sex-linked markers that mapped on Y chromosome were aligned to three different promoter regions of <i>Rana rugosa</i> CYP19A1 gene, which might be considered as a candidate gene to trigger sex determination in <i>A</i>.<i> mantzorum</i>.</span></p>
SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum
<p>The Manila clam <i>Ruditapes philippinarum</i>, a major cultured shellfish species, is threatened by infection with the microparasite <i>Perkinsus olseni</i>, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against <i>P. olseni</i>, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR.</p> <p>A mixed-family cohort of potentially 1479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of <i>P. olseni</i> had previously been reported. Growth and parasite load were monitored every month and, after one year, more than 1000 individuals were collected and DNA and phenotype records.</p> <p>A 245-SNP panel was developed using candidate markers obtained from a pooled sequencing approach on two DNA samples from all the potential parents and from a Venice lagoon clam population. For 246 individuals of the mixed-family F1, sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.20 – 0.30) was estimated for growth traits, while parasite load showed high heritability, estimated at 0.52. No significant genetic correlations were found between growth-associated traits and parasite load.</p> <p>Overall, the study shows high potential for selecting clams resistant to parasite<i> </i>load<i>.</i> Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.</p>
FIGURE 1. Acuscercus eudaldoleondiazi n. gen et n in Studies in Neotropical Pseudophyllinae: A new genus of Cocconotini from the ColombianAndes and new subfamily assignment of the Dominican genus Anacaona (Tettigoniidae: Pseudophyllinae: Cocconotini)
FIGURE 1. Acuscercus eudaldoleondiazi n. gen et n. sp. male. A. Habitus in lateral view. B. Frons. C–D. Head and thorax in lateral and dorsal view respectively.
FIGURE 4. Kumepagurus kaikata n in A new species of pagurid hermit crab assigned to the genus Kumepagurus Komai & Osawa, 2012 (Decapoda: Anomura: Paguroidea) from the Kaikata Seamount Izu-Ogasawara Arc, Japan
FIGURE 4. Kumepagurus kaikata n. sp., holotype, ovigerous female (sl 1.7 mm), CBM-ZC 16169. A, right pereopod 2, lateral view; B, same, dactylus, mesial view (only mesial setae illustrated); C, left pereopod 3, lateral view; D, same, dactylus, mesial view (only mesial setae illustrated).
FIGURE 1. Kumepagurus kaikata n in A new species of pagurid hermit crab assigned to the genus Kumepagurus Komai & Osawa, 2012 (Decapoda: Anomura: Paguroidea) from the Kaikata Seamount Izu-Ogasawara Arc, Japan
FIGURE 1. Kumepagurus kaikata n. sp., A–E, G, holotype, ovigerous female (sl 1.7 mm), CBM-ZC 16169; F, paratype, male (sl 1.8 mm), CBM-ZC 16170. A, shield, carapace lateral lobe and cephalic appendages, dorsal view; B, left maxilliped 3, lateral view; C, same, ischium, ventral view; D, left pereopod 4, lateral view; E, thoracic sternite 6, ventral view; F, coxae of pereopods 5 and thoracic sternite 8, ventral view, showing development of sexual tubes; G. telson, dorsal view.
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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.