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Fig. 7 in A morphometric approach to the specific separation of the humeri and femora of Dicraeosaurus from the Late Jurassic of Tendaguru,Tanzania
Fig. 7. Procrustes fits (A, C) and PCA values (B, D) of Dicraeosaurus humeri. A. Procrustes fits of Dicraeosaurus sattleri (open circles) and Dicraeosaurus hansemanni (crosses), anterior face. B. PCA values of same taxa, large circle is mean value of deviance for D. sattleri; 1, MB.R.2631; 2, MB.R.2655; 3 , MB.R.2657; 4, MB.R.4912. C. Procrustes fits of D. sattleri (open circles) and D. hansemanni (crosses), posterior face. D. PCA values of same taxa, large circle is mean value of deviance for D. sattleri; 1, MB.R.2631; 2, MB.R.2634; 3, MB.R.2655; 4, MB.R.2657; 5, MB.R.4912.
Fig. 6 in A morphometric approach to the specific separation of the humeri and femora of Dicraeosaurus from the Late Jurassic of Tendaguru,Tanzania
Fig. 6. Thin-plate Splines of femora of dicraeosaurid dinosaurs Dicraeosaurus and Amargasaurus. A. Reference shape of femora of Dicraeosaurus. B. MB.R.2638, Dicraeosaurus sattleri in comparison with reference shape slightly shortened femoral head, 4th trochanter proximally displaced and longer tibial condyles. C. MB.R.4886.92, Dicraeosaurus hansemanni in comparison with reference shape femoral head slightly medially and proximally enlarged and distal condyli approaching each other. D. MB.R.4886.93, D. hansemanni in comparison with reference shape 4th trochanter displaced distally and medially, and distal condyles approaching each other. E. Reference shape of femur of Amargasuarus cazaui, MACN N-15. Printouts from tpsSplin (Rohlf 2004a). Not to scale.
Fig. 4 in A morphometric approach to the specific separation of the humeri and femora of Dicraeosaurus from the Late Jurassic of Tendaguru,Tanzania
Fig. 4. Landmark positions used for the bones of Dicraeosaurus and Amargasaurus. A. Left humerus in anterior aspect, 1. and 4. maximum width of proximal extremity, measured on medial and lateral margin of proximal extremity; 2. and 3. latero-medial width of articular surface of humeral head (3. is also proximal border of deltopectoral crest); 5. peak (highest elevation) of deltopectoral crest; 6. and 7. medial and lateral margin of shaft at distal end of deltopectoral crest; 8. and 11. maximum width of distal extremity, measured on medial and lateral margin of distal extremity; 9. distal medial ridge; 10 distal lateral ridge. B. Left humerus posterior aspect. 1. and 4. maximum width of proximal extremity, measured on medial and lateral margin of proximal extremity; 2. and 3. latero-medial width of articular surface of humeral head; 5. and 6. minimum shaft diameter measured at the medial and lateral margin of the shaft; 7. and 11. maximum width of distal extremity, measured on medial and lateral margin of distal extremity; 8–10. boundary of olecranon fossa. C. Left femur posterior aspect. 1. medial margin of femoral head; 2. lateral margin of femoral head; 3. greater trochanter; 4. lesser trochanter (lateral end); 5. peak (maximum elevation) of 4th trochanter; 6. and 7. minimum shaft diameter measured at the medial and lateral margin of the shaft (7. is also distal end of 4th trochanter); 8. and 12. maximum width of distal extremity, measured on medial and lateral margin of distal extremity; 9. centre of fibular condyle; 10. maximum elevation of lateral condyle; 11. maximum elevation of tibial condyle.
Fig. 3 in A morphometric approach to the specific separation of the humeri and femora of Dicraeosaurus from the Late Jurassic of Tendaguru,Tanzania
Fig. 3. Studied sample of femora of dicraeosaurid dinosaurs Dicraeosaurus in posterior aspect. Dicraeosaurus hansemanni (A, B), Dicraeosaurus sattleri (C–G), and Amargasaurus cazaui (H). A. MB.R.4886.92, right femur. B. MB.R.4886.93 left femur. A and B belong to the mounted skeleton "m". C. MB.R.2695, right femur. D. MB.R.2696, right femur. E. MB.R.2697, right femur. F. MB.R.2638, left femur. G. MB.R.2915, left femur. H. MACN-N 15, left femur. Scale bars 20 cm.
Fig. 2 in A morphometric approach to the specific separation of the humeri and femora of Dicraeosaurus from the Late Jurassic of Tendaguru,Tanzania
Fig. 2. Studied sample of humeri of dicraeosaurid dinosaurs Dicraeosaurus and Amargasaurus in anterior aspect. Dicraeosaurus hansemanni (A), Dicraeosaurus sattleri (B–E), and Amargasaurus cazaui (F). A. MB.R.4912, right humerus. B. MB.R.2631, right humerus. C. MB.R.2634, right humerus. D. MB.R.2655, left humerus. E. MB.R.2657, left humerus. F. MACN-N 15, right humerus. Scale bars 10 cm.
MAGE-A3-specific T-cells
<p>Single-cell RNA-seq data of MAGE-A3-specific T-cells genereated with the BD Rhapsody™ system.</p> <p>Donor information: 3 healthy subjects, 2 male (SampleTag01, SampleTag03), 1 female (SampleTag02).</p> <p>Cell preparation: MAGE-A3-specific T-cells were obtained via a Tetramer-based sorting of the naturally-occuring anti-CD3 and anti-CD28-activated T-cells co-cultured with the Dendritic cells that were maturated by a KVAELVHFL peptide. </p> <p>Single-cell analysis system: BD Rhapsody™</p> <p>Library strategy: 5' mRNA sequencing</p> <p>Library preparation protocol: BD Rhapsody™ TCR/BCR Full Length, Targeted mRNA, and Sample Tag Library Preparation</p> <p>mRNA panel: BD Rhapsody™ Immune Response Panel HS</p> <p>BD Pipeline version: 1.12</p>
Figure 4 in First reports of species-specific ant resemblance in heteronotine treehoppers (Hemiptera: Membracidae: Heteronotinae)
Figure 4. Comparison of morphological measurements of Cephalotes atratus (Linnaeus, 1758), workers (circles, n = 10) and females of Heteronotus fabulosus Boulard, 1981 (cross-marks, n = 2); L = length between apex of pronotal spine (CS in membracids) and apex of abdomen (NT in membracids) as indicated by "L" in Fig. 3C; blue = relationship between "L" and width between apices of pronotal spines (CS in membracids); orange = relationship between "L" and width abdomen (width NT in membracids); grey = relationship between "L" and pronotal width in ant (as indicated in Fig. 3B) or width of black pronotal area in membracids (as indicated by "3" in Fig. 3D); green = relationship between "L" and actual pronotal width of membracids (as indicated by "4" in Fig. 3D).
Figure 2. Heteronotus fabulosus Boulard, 1981. Both photographs taken during the dry season, 5 Sep 2021. A in First reports of species-specific ant resemblance in heteronotine treehoppers (Hemiptera: Membracidae: Heteronotinae)
Figure 2. Heteronotus fabulosus Boulard, 1981. Both photographs taken during the dry season, 5 Sep 2021. A) Habitat at edge of a Chiquitano forest fragment, sampled branches of host tree Swartzia jorori tree (Fabaceae) indicated by white arrow. B) Putative nymph of H. fabulosus, tended by worker of Cephalotes atratus (Linnaeus, 1758).
Figure 3. Comparison between potential ant model and membracid mimic. Both specimens have the same body length. A–B in First reports of species-specific ant resemblance in heteronotine treehoppers (Hemiptera: Membracidae: Heteronotinae)
Figure 3. Comparison between potential ant model and membracid mimic. Both specimens have the same body length. A–B) Cephalotes atratus (Linnaeus, 1758), worker. A) Habitus, dorsal. B) Head and anterior part of mesothorax, dorsal. C–D) Heteronotus fabulosus Boulard, 1981. C) Habitus, dorsal. CS = Cornus suprahumeralis; L = length between apex of CS and apex of NT; NPS = Spina nodus primus; NT = Nodus terminalis; PS = Spina pedunculus. D) Anterior part of pronotum; head, wings and legs omitted. E) Cephalotes atratus worker habitus, lateral. F) Heteronotus fabulosus habitus, lateral. Numbered structures in the figures reference the numbering system used for morphological comparisons in Figure 4.
Figure 1. Study area. A in First reports of species-specific ant resemblance in heteronotine treehoppers (Hemiptera: Membracidae: Heteronotinae)
Figure 1. Study area. A) Bolivia. B) Sub-Andean area at the Bolivian orocline; 1, Santa Cruz de la Colina, Urubo, Santa Cruz department; map produced with QGIS (version 2.14.3, http://www.qgis.org/en/site), ecoregions according to the regionalization by Navarro and Ferreira (2011).
Fig 1 in Host specificity evaluation for Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae) on ornamental Ficus (Rosales: Moraceae)
Fig 1. Cage setup for Ficus benjamina variety choice test with Gynaikothrips uzeli in the greenhouse (year 2).
Fig. 4 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 4. Geographic distribution of the phylogenetic groups of avian piroplasmids (based on the 18S rRNA gene). Map prepared based on information provided in Criado et al. (2006), Yabsley et al. (2006, 2009), Jefferies et al. (2008), Paparini et al. (2014), Quillfeldt et al. (2014), Martínez et al. (2015), Montero et al. (2016) and Chavatte et al. (2017).
Fig. 2 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 2. Maximum likelihood phylogenetic tree of the ITS-1 (445 bp) and ITS-2 regions sequences (290 bp) of select avian-infecting Babesia lineages. Sequences identified in this study are emphasized in red, and those of other avian-infecting lineages are shown in blue. For each sequence, the following information is provided: morphospecies (individual identification or Genbank code) host species. Branch lengths are drawn proportionally to evolutionary distance (scale bar shown corresponds to both trees). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 3 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 3. Distribution of the phylogenetic groups of avian piroplasmids (based on the 18S rRNA gene) in relation to the phylogeny of avian orders (based on multiple nuclear genes). Avian orders investigated in this study are shown in red, and other avian orders known to host piroplasmids are shown in blue. Avian phylogeny was adapted from Yuri et al. (2013). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 1 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 1. Maximum likelihood phylogenetic tree of the 18S rRNA gene sequences (1450 bp) of the studied Babesia lineages. Sequences obtained in this study are emphasized in red, and those of other avian-infecting lineages are shown in blue. For each sequence, the following information is provided: morphospecies (individual identification or GenBank code) host species. For avian-infecting lineages, the host order is indicated with colored circles (see legend). Branch lengths are drawn proportionally to evolutionary distance. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
OLS, OntoPortal, Skosmos - API mapping specifications for API Gateway and Terminology Service Suite
<p>A set of initial API endpoints have been defined for the central API Gateway together with the initial set of service wrappers for each of the covered technologies (OLS, OntoPortal and Skosmos). This involves detailing the call URL structures, HTTP methods, service parameters, authentication methods, and expected response formats for each type of endpoint. <span>This document outlines the various backend APIs for the API Gateway and provides guidance on how to harmonise and map them. The API Gateway is used to provide information in a format that can be utilised by the widgets within the Terminology Service Suite (TSS). Each table in this document is related to one widget of the TSS.</span></p>
FIGURE 6 in A Phylogenetic Overview of Sponge-inhabiting Barnacles and Their Host Specificity (Crustacea, Cirripedia)
FIGURE 6. Bayesian phylogenetic tree based from CO1 and H3 concatenated sequence data (869 bp). Numbers at nodes represent Bayesian posterior probability values. Numbers on branches represent substitutions per site on that branch. (A) Clade of Acastinae from Philippines and Madagascar in Phyllospongiinae hosts (blue-shaded box); (B) Clade of Bryozobiinae (3 genera) barnacles from Madagascar in encrusting sponge hosts Clathria (Microciona) sp. and Monanchora aff. unguiculata (orange-shaded box); (C) Clade of Eoatria sp. (Bryozobiinae) and 3 undescribed Acastinae barnacles in encrusting sponges (purple-shaded box). All barnacle taxa in this analysis are in the family Archaeobalanidae. All of the taxa identified as members of the Acastinae appear to be undescribed species. Semibalanus balanoides is used as the outgroup in the analysis and is not a sponge-inhabiting species. Numbers on taxon labels are CASIZ specimen catalog numbers.
suggests that northern specimens of R. barnardi should be reexamined to confirm their specific identity. MAP 154. Distribution of Rhoptropus sp. in Angola. in Diversity and Distribution of the Amphibians and Terrestrial Reptiles of Angola Atlas of Historical and Bibliographic Records (1840-2017)
suggests that northern specimens of R. barnardi should be reexamined to confirm their specific identity. MAP 154. Distribution of Rhoptropus sp. in Angola.
Figure 10. Sensitivity and specificity of different bands-Classification of Human Emotion from Deap EEG Signal Using Hybrid Improved Neural Networks with Cuckoo Search
<p>Figure10 has shown in sensitivity and specificity of different neural network which is used<br> to explain how exactly the emotions are classified into groups and accuracy value shown in above<br> table 3.</p>
Updated spiny mouse transcriptome assembly (now includes embryo-specific transcripts)
<p><strong>Summary</strong></p> <p>Updated spiny mouse transcriptome. Embryo-specific contigs generated from BioProject PRJNA436818 were added to the Trinity_v2.3.2 spiny mouse <em>de novo </em>transcriptome assembly (https://doi.org/10.5281/zenodo.808870).</p> <p> </p> <p><strong>Methods</strong></p> <p>Embryos were collected from female spiny mice (n=12) in accordance with the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes with approval from the Monash Medical Centre Animal Ethics Committee. Female dams were staged from delivery of their previous litter (spiny mice conceive their next litter approximately 12h postpartum) and culled at specific time-points for embryo retrieval at the required stage: 2-cell at 48h postpartum (n=4), 4-cell at 52h postpartum ('early' 4-cell; n=2) or at 68h postpartum ('late 4-cell'; n=2), and 8-cell at 72h postpartum (n=4). Embryos were snap frozen in cell lysis solution per the Nugen SoLo protocol (version M01406v3; available from NuGEN). After ligation of cDNA, qPCR was performed on all samples to determine the number of amplification cycles required to ensure that amplification was in the linear range. Based on these results, each sample was amplified using 24 cycles. Final libraries were quantitated by Qubit and size profile determined by the Agilent Bioanalyzer. All libraries were in the expected size range (~320-360 bp). Custom 'AnyDeplete' rRNA depletion probes were designed and produced by NuGEN Technologies, Inc (San Carlos, CA, USA) using rRNA sequences from our reference transcriptome (Mamrot et al., 2017; https://doi.org/10.5281/zenodo.808870). Prior to use, efficacy and off-target effects of the rRNA depletion probes were examined <em>in silico</em> by NuGEN. Samples were loaded using c-Bot (200pM per library pool) and run on 2 lanes of an Illumina HiSeq 3000 8-lane flow-cell. PhiX spike-in was not used directly due to incompatibility with the custom rRNA depletion probes, however it was incorporated into other lanes of the same HiSeq 3000 run. RNA-Seq data (100bp, paired-end reads) are available from the NCBI as Bioproject PRJNA436818.</p> <p>The quality of RNA-Seq reads was assessed using FastQC v0.11.6 (<a href="https://github.com/s-andrews/FastQC">https://github.com/s-andrews/FastQC</a>; 50f0c26), with MultiQC v1.4 (<a href="https://github.com/ewels/MultiQC">https://github.com/ewels/MultiQC</a>; baefc2e) reports available from Github (<a href="https://github.com/jpmam1">https://github.com/jpmam1</a>) (Ewels et al., 2016). Adapter sequences were trimmed from the reads using trim-galore v0.4.2 (<a href="https://github.com/FelixKrueger/TrimGalore">https://github.com/FelixKrueger/TrimGalore</a>; d6b586e), implementing cutadapt v1.12 (<a href="https://github.com/marcelm/cutadapt">https://github.com/marcelm/cutadapt</a>; 98f0e2f). Reads with a quality scores lower than 20 and read pairs in which either forward or reverse reads were trimmed to fewer than 35 nucleotides were discarded. Further trimming of poor quality reads was conducted using Trimmomatic v0.36 (<a href="http://www.usadellab.org/cms/index.php?page=trimmomatic">http://www.usadellab.org/cms/index.php?page=trimmomatic</a>) with settings "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 AVGQUAL:25 MINLEN:35" (Bolger et al., 2014). Nucleotides with quality scores lower than 3 were trimmed from the 3’ and 5’ read ends. Reads with an average quality score lower than 25 or with a length of fewer than 35 nucleotides after trimming were removed. Error correction of reads was performed using Rcorrector v1.0.2 (<a href="https://github.com/mourisl/Rcorrector">https://github.com/mourisl/Rcorrector</a>; 144602f) (Song et al., 2015). FastQC was used to assess the improvement in read quality after trimming adapter removal; MultiQC reports are available from Github (<a href="https://github.com/jpmam1">https://github.com/jpmam1</a>).</p> <p>Error corrected reads were assembled using Trinity v2.4.0 (<a href="https://github.com/trinityrnaseq/trinityrnaseq">https://github.com/trinityrnaseq/trinityrnaseq</a>; 1603d80) with settings "--max_memory 400G, --CPU 32 and --full_cleanup" (Haas et al., 2013). Assembly statistics were computed using the TrinityStats.pl from the Trinity package, and summary statistics are provided in Table S1. All reads were aligned to this transcriptome assembly using Bowtie2 v2.2.5 (<a href="https://github.com/BenLangmead/bowtie2">https://github.com/BenLangmead/bowtie2</a>; e718c6f) with settings: "--end-to-end, --score-min L,-0.1,-0.1, --no-mixed, --no-discordant, -k 100, -X 1000, --time, -p 24" (Langmead & Salzberg, 2012).</p> <p>Read-supported contigs were identified within the embryo-specific Trinity <em>de novo </em>transcriptome assembly using samtools "idxstats" v1.5 (contigs with >=1 reads aligning were retained) (<a href="https://github.com/samtools/samtools">https://github.com/samtools/samtools</a>; f510fb1) (Li et al., 2009). The read-supported contigs from the embryo-specific assembly (n=54,660) were added to the reference spiny mouse transcriptome assembly previously described (Mamrot, J., Legaie, R., Ellery, S.J., Wilson, T., Seemann, T., Powell, D.R., Gardner, D.K., Walker, D.W., Temple-Smith, P., Papenfuss, A.T. and Dickinson, H., 2017. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). Scientific Reports, 7(1), p.8996).</p> <p>The updated transcriptome is comprised of 2,274,638 transcripts in total.</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.