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Figure 1 from: Rosa G, Penny S, Andreone F, Crottini A, Holderied M, Rakotozafy L, Schwitzer C (2014) A new species of the Boophis rappiodes group (Anura, Mantellidae) from the Sahamalaza Peninsula, northwest Madagascar, with acoustic monitoring of its nocturnal calling activity. ZooKeys 435: 111-132. https://doi.org/10.3897/zookeys.435.7383
Figure 1 - The Sahamalaza Peninsula in northwest Madagascar, indicating the study sites of (A) Ankarafa Forest, (B) Antafiabe Village, (C) Anabohazo Forest and (D) Betsimpoaka village. Source: Madagascar National Parks (MNP).
Figure 3 from: Rosa G, Penny S, Andreone F, Crottini A, Holderied M, Rakotozafy L, Schwitzer C (2014) A new species of the Boophis rappiodes group (Anura, Mantellidae) from the Sahamalaza Peninsula, northwest Madagascar, with acoustic monitoring of its nocturnal calling activity. ZooKeys 435: 111-132. https://doi.org/10.3897/zookeys.435.7383
Figure 3 - Breeding activity of Boophis ankarafensis sp. n.: A Paratype MRSN A6976 B–C Vocalising males sitting on leaves and on a branch (specimens not collected) D Male holotype MRSN A6973 and female A6974 E Couple in axillary amplexus.
Figure 2 from: Rosa G, Penny S, Andreone F, Crottini A, Holderied M, Rakotozafy L, Schwitzer C (2014) A new species of the Boophis rappiodes group (Anura, Mantellidae) from the Sahamalaza Peninsula, northwest Madagascar, with acoustic monitoring of its nocturnal calling activity. ZooKeys 435: 111-132. https://doi.org/10.3897/zookeys.435.7383
Figure 2 - Life colouration of Boophis ankarafensis sp. n.: A Rostral view of a male paratype (MRSN A6975) B Dorsal view of the same male C Female specimen in resting position on a leaf (specimen not collected) D Dorso-lateral view of the holotype with day-time colouration (MRSN A6973).
Figure 2 from: Salazar-Moncada DA, Calle-Osorno J, Ruiz-Lopez F (2015) Morphological and molecular study of Symphyla from Colombia. ZooKeys 484: 121-130. https://doi.org/10.3897/zookeys.484.8363
Figure 2 - Ventral view of a Colombian symphylan. Presence of sternal appendages behind coxal sacs (arrows).
Figure 1 from: Salazar-Moncada DA, Calle-Osorno J, Ruiz-Lopez F (2015) Morphological and molecular study of Symphyla from Colombia. ZooKeys 484: 121-130. https://doi.org/10.3897/zookeys.484.8363
Figure 1 - Colombian symphylan. A Heart-shaped head and antennae B Tömosvary organ (arrow) C Last scuta margin with a U-shaped groove (arrow).
Comparison of re-called Albacore and Flappie sequences from E. coli K-12 MG1655
<p>I used the first few (545) original Fast5 files from Nick Loman's ultra-long read E. coli K-12 MG1655 R9.4 sequencing run. See the blog post <a href="http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/">here</a>. Direct link to the complete fast5 dataset <a href="http://s3.climb.ac.uk/nanopore/Ecoli_MinKNOW_1.4_RAD002_Sambrook.tar">here</a>.</p> <p>Program versions:</p> <p>* Albacore 2.1.10</p> <p>* Flappie 1.0.0-0048dfd</p> <p>The example alignment was carried out using seaview (1:4.6.1.2-2), and visualised using spiralign from my <a href="https://gitlab.com/gringer/bioinfscripts/">bioinfscripts</a> repository (see source code in this archive):</p> <p> $ spiralign.r -size 2000x2000 -noalign -noborder -loops 12.75 -outfmt png -type nucl -title "Flappie vs Albacore\n(Ecoli_MG1655)" aligned_all_ddea.fa</p> <p>Flappie was distributed across multiple processing threads using GNU parallel:</p> <p> $ ls Ecoli_MinKNOW_1.4_RAD002_Sambrook/0/nanopore2_20170301_FNFAF09967_MN17024_mux_scan_170301_MG1655_PC_RAD002_76964_ch* | parallel --group -j 10 -L 1 ~/install/flappie/flappie | gzip > called_flappie_Ecoli_MinKNOW_1.4_RAD002_Sambrook.fq.gz</p> <p> </p> <p>Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.</p>
1 in Intraspecific Call Variation in the Mimic Poison Frog Ranitomeya imitator
1+ tanh 2x ae ‾c ŋ= +ŋ min 2 ŋ max ‾ 1 ŋmin
VCF of structural variant calls of Nanopore data aligned to dm6 reference genome
<p>Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the <em>dl</em>-<em>49</em> <em>chrX</em> inversion in <em>D</em>. <em>melanogaster</em>. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs are completely suppressed within 500 kb of inversion breakpoints, are severely reduced within 2 Mb of an inversion breakpoint, and increase above wildtype levels 2–4 Mb from the breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, occur at wild-type levels near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break location or frequency. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.</p>
Dataset for the manuscript "In silico evaluation of variant calling methods for bacterial whole genome sequencing"
<p>Input data and associated analysis code for reproducing results reported in the manuscript.</p>
Figures 4–5 in Individual variation in the advertisement call of Aplastodiscus albosignatus (Anura: Hylidae) is correlated with body size and environmental temperature
Figures 4–5. Spectrogram and oscillogram of two advertisement calls of the same male of Aplastodiscus albosignatus: (4) call with the dominant frequency in the first harmonic (= minimum frequency); (5) call with the dominant frequency in the third harmonic. Male recorded on January 14, 2020, voucher of specimen RLUTF 1220, voucher of recording FNJV 45563, 4.7 g, 44.8 mm, 18.1 °C.
Fig. 1 in Calling songs of sympatric and allopatric populations of Cicada barbara and C. orni (Hemiptera: Cicadidae) on the Iberian Peninsula
Fig. 1. Allopatric populations of Cicada barbara (dark circles) and C. orni (empty circles), and sympatric populations of both species (triangles) sampled on the Iberian Peninsula
"This was on this huge market Kikar Shabat in Jerusalem. Iwas on holiday in Israel during a Jewish Festival called Sukkot. I live in England and I'm a Jew. Iwas in the market to buy lulav and estrog. It was a huge traditional festive fair opened a week after Sukkot. It was my first trip to Israel since Iwas a teenager. There was bustle, a lot of Jews. Irecorded this sound, because Iwanted to have a souvenir, to keep this experience of this bustle and hubbub". [Mike/Sparrer]11 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"This was on this huge market Kikar Shabat in Jerusalem. Iwas on holiday in Israel during a Jewish Festival called Sukkot. I live in England and I'm a Jew. Iwas in the market to buy lulav and estrog. It was a huge traditional festive fair opened a week after Sukkot. It was my first trip to Israel since Iwas a teenager. There was bustle, a lot of Jews. Irecorded this sound, because Iwanted to have a souvenir, to keep this experience of this bustle and hubbub". [Mike/Sparrer]11
TCGA combined mutation calls files
Open the record for dataset details and reuse information.
A Study to Test Different Doses of BI 836880 in Patients With an Eye Disease Called Wet Age-related Macular Degeneration (wAMD)
ClinicalTrials.gov study NCT03861234. IPD Sharing: NO. Countries: 3. Publications: 0.
A Study to Describe the Breast Cancer Patient Population, Treatment, and Results in Indian Patients Receiving Combinations of the Medicines Called Palbociclib for Advanced Breast Cancer
ClinicalTrials.gov study NCT05584644. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study to Learn About the Study Medicine Called Nirmatrelvir/Ritonavir in People Who Are Healthy Volunteers Co-administered the Medicine Rosuvastatin
ClinicalTrials.gov study NCT05898672. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study to Assess a New Medicine Called IPN01195 When Administered Alone in Adults With Advanced Solid Tumours
ClinicalTrials.gov study NCT06833008. IPD Sharing: YES. Countries: 4. Publications: 0.
Audiologic Assessment of Call Center Operators
ClinicalTrials.gov study NCT05728203. IPD Sharing: UNDECIDED. Countries: 0. Publications: 1.
My Care My Call: Peer-Led Health Empowerment Training in Chronic Spinal Cord Injury
ClinicalTrials.gov study NCT02878070. IPD Sharing: NO. Countries: 0. Publications: 1.
A Study to Understand the Effect of a Study Medicine Called ARV-471 on Dabigatran Etexilate in Healthy Adults
ClinicalTrials.gov study NCT05673889. IPD Sharing: NO. Countries: 1. Publications: 0.
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.