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3,696 results for “reference”
FIGURE 7. A–H in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 7. A–H) Vein axils (abaxial leaf surface). Tuft of hairs are distinctly visible in (B), (D), (H). A) V. vinifera; B) V. riparia; C–D) V. ×instabilis; E) V. rupestris; F) V.×ruggerii; G) V.cinerea; H) V. ×koberi. All photos by Michele Zilioli.
FIGURE 6. A, C–E, G in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 6. A, C–E, G) Petiole insertion (abaxial surface); B, F, H) petiole insertion detail. A) V. riparia; B–D) V. ×instabilis; E–F) V. rupestris; G–H) V.×ruggerii. All photos by Michele Zilioli.
hg38 reference and annotation files
<p>This repo contains reference and annotation files for hg38. We are following the [TOPMed pipeline](https://github.com/broadinstitute/gtex-pipeline/blob/master/TOPMed_RNAseq_pipeline.md). Reach out to Arushi Varshney at arushiv AT umich DOT edu if you have any questions.</p> <p>Files:</p> <p>1. bwa index = bwa.tar.gz</p> <p>2. star index = star.tar.gz</p> <p>3. ENCODE blacklist = blacklist.tar</p> <p>4. gencode v30 annotations = gencode.tar.gz</p> <p>5. containers with STAR (RNA) and BWA (ATAC) = containers.tar.gz</p> <p>Notes on these files:<br> ### hg38 fasta:<br> I downloaded the TOPMed fasta tar [Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.tar.gz](https://personal.broadinstitute.org/francois/topmed/Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.tar.gz) as use this as-is. The TOPMed GitHub describes that they obtained the Broad institute's GRCh38 reference, removed ALT, HLA and Decoy contigs, and added ERCC spike-in reference annotations. Refer to their [README](https://github.com/broadinstitute/gtex-pipeline/blob/master/TOPMed_RNAseq_pipeline.md) for more details. They don't mention PARs but we checked the reference files and both chrY PARs are hard masked - as [ENCODE](https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/) also recommends.<br> ### Gencode v30 gene annotations: gencode.tar.gz<br> I downloaded the file [gencode.v30.annotation.gtf.gz](https://www.gencodegenes.org/human/release_30.html) from the gencode website, and downloaded the file [ERCC92.genes.patched.gtf](https://personal.broadinstitute.org/francois/resources/). I then appended the ERCC patched gtf to the gencode annotation gtf<br> ```<br> gunzip gencode.v30.annotation.gtf.gz<br> cat gencode.v30.annotation.gtf ERCC92.genes.patched.gtf > gencode.v30.annotation.ERCC92.gtf<br> ```<br> ### STAR index: star.tar.gz; container with star in containers.tar.gz<br> A STAR index is shared on the TOPMed GitHub, but it was generated for STAR version STAR_2.6.1d. Since I've been using the version 2.7.3a, I followed their steps to generate the STAR reference again. I used the gencode gtf described above and generated the STAR index.</p> <p>```<br> STAR --runMode genomeGenerate --genomeDir STAR_genome_GRCh38_noALT_noHLA_noDecoy_ERCC_v30_test --genomeFastaFiles Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta --sjdbGTFfile gencode.v30.annotation.ERCC92.gtf --sjdbOverhang 100 --runThreadN 10<br> ```<br> ### BWA index: bwa.tar.gz<br> I generated the BWA index using the fasta above<br> ```</p> <p>ln -s Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta hg38.fa<br> bwa index hg38.fa<br> ```<br> <br> ### ENCODE Blacklist: blacklist.tar<br> I used the blacklist [here](https://theparkerlab.med.umich.edu/data/arushiv/hg38_references_annots/blacklist/) that I obtained from this [Kundaje website](https://sites.google.com/site/anshulkundaje/projects/blacklists).</p>
Pragmatic prediction in the processing of referring expressions containing scalar quantifiers
<p>Data and analysis scripts pertaining to a study by Macuch Silva & Franke (submitted).</p>
Figure 4 in Avian mortality due to power lines in the Canary Islands with special reference to the steppe-land birds
Figure 4. Distribution of power lines, steppe habitat and carcasses of stone curlew, Burhinus oedicnemus insularum, on the Canary Islands of Fuerteventura and Lanzarote.
Figure 2 in Avian mortality due to power lines in the Canary Islands with special reference to the steppe-land birds
Figure 2. Distribution of number of dead birds (carcasses) found per family. 1, Otididae; 2, Burhinidae; 3, Unidentified; 4, Columbidae; 5, Laridae; 6, Glareolidae; 7, Corvidae; 8, Procellariidae; 9, Ardeidae; 10, Phasianidae; 11, Motacillidae; 12, Ciconiidae; 13, Accipitridae; 14, Falconidae; 15, Upupidae; 16, Hirundinidae; 17, Scolopacidae; 18, Pteroclididae; 19, Tytonidae; 20, Meropidae; 21, Alaudidae; 22, Muscicapidae; 23, Laniidae; 24, Fringillidae.
Figure 1 in Avian mortality due to power lines in the Canary Islands with special reference to the steppe-land birds
Figure 1. Location of study sites and distribution of power lines and steppe habitat on the Canary Islands of Fuerteventura and Lanzarote.
Figure 3 in Avian mortality due to power lines in the Canary Islands with special reference to the steppe-land birds
Figure 3. Distribution of power lines, steppe habitat and carcasses of houbara bustard, Chlamydotis undulata fuertaventurae, on the Canary Islands of Fuerteventura and Lanzarote.
data set related to article Suicidal ideation, suicidal attempts and non-suicidal self-injuries in referred adolescents
<p>This record contains raw data to article Suicidal ideation, suicidal attempts and non-suicidal self-injuries in referred adolescents</p>
data set related to article Suicidal ideation and suicidal attempts in referred adolescents with high functioning autism spectrum disorder and comorbid bipolar disorder: A pilot study
<p>This record contains raw data related to article Suicidal ideation and suicidal attempts in referred adolescents with high functioning autism spectrum disorder and comorbid bipolar disorder: A pilot study</p>
FIGURE 28 in New cytogenetic data on Coreoidea (Hemiptera: Heteroptera) with special reference to Coreidae
FIGURE 28. Phylogenetic relationships among the tribes or subfamilies (modified after Schaefer 1965, 1982; Li 1997) and cytogenetic characteristics of members of Coreidae (modal autosomal diploid number, sex chromosome system, and number of species cytogenetically analyzed in each subfamily)
FIGURES 13–21. 13-17 in New cytogenetic data on Coreoidea (Hemiptera: Heteroptera) with special reference to Coreidae
FIGURES 13–21. 13-17. Male meiosis of A. scaber; 13, pachytene; 14. diffuse stage; 15. diakinesis; 16. metaphase I; 17. metaphase II. 18-21. Male meiosis of P. longirostris; 18,19. diakinesis; 20. metaphase I; 21. metaphase II. Bar= 10 µm.
FIGURES 1–12. 1–6 in New cytogenetic data on Coreoidea (Hemiptera: Heteroptera) with special reference to Coreidae
FIGURES 1–12. 1–6. Male meiosis of S. femoralis; 1. pachytene; 2, 3. diffuse stage; 4, diplotene; 5, metaphase I; 6. metaphase II. 7-12. Male meiosis of Hy. orientalis; 7. pachytene; 8, 9. diffuse stage; 10. diakinesis; 11. metaphase I; 12. metaphase II. Bar= 10 µm.
FIGURES 22–27. 22–24 in New cytogenetic data on Coreoidea (Hemiptera: Heteroptera) with special reference to Coreidae
FIGURES 22–27. 22–24. Male meiosis of C. graminis; 22. diplotene; 23. diakinesis; 24. metaphase II. 25-27. Male meiosis of Ho. bannaensis; 25. pachytene; 26 metaphase I; 27. metaphase II. Bar= 10 µm.
FIG. 45 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 45. SEM photographs of species of Limatula. (a) L. louiseae; (b) L. margaretae; (c) L. smithi; (d) L. celtica..
FIG. 44. Limea argentinea. Sta. 237 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 44. Limea argentinea. Sta. 237, (a) semi-diagrammatic view of the anatomy from the right side of a juvenile specimen; (b) ventral view of the lips of the specimen in figure 42. Scale bars: 1 mm.
FIG. 42. Limea argentinea. Sta. 237 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 42. Limea argentinea. Sta. 237, lateral view of the right valve of the type specimen. Scale bar: 1 mm.
FIG. 40. Limea sarsi. Sta. z397 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 40. Limea sarsi. Sta. z397, semi-diagrammatic internal view of the detached left mantle and gill. Scale bar: 1 mm.
FIG. 46 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 46. SEM photographs of species of Limatula and Limea. (a) Limatula thalassae; (b) Limatula laminifera; (c) Limea lirata; (d) Limea sarsi.
FIG. 43. Limea argentinea. Sta. 237 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 43. Limea argentinea. Sta. 237, (a) internal view of left hinge; (b) dorsal view of right hinge. Scale bars: 1 mm.
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.