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9,097 results for “wild”
FIGURE 2 in Chewing lice (Phthiraptera: Amblycera and Ischnocera) from wild birds in southern Vietnam, with descriptions of two new species
FIGURE 2. Brueelia binhchauensis: A, male genitalia. B, dorso-ventral view of head of male. C, dorsal view of male terminalia. D, ventral view of female terminalia. Scales = 0.10 mm for all figures.
FIGURE 6. Nemachilichthys rueppelli WILD-15 in Redescription of Nemachilichthys rueppelli, a senior synonym of N. shimogensis (Teleostei: Nemacheilidae)
FIGURE 6. Nemachilichthys rueppelli WILD-15-PIS-217 (Koyna River, 61.3 mm SL) in (A) lateral, (B) dorsal and (C) ventral view.
Data Figures Indicators of the 'wild seafood' provisioning ecosystem service based on the surplus production of commercial fish stocks
<p>This excel sheet contains the underlying data for the Figures that are presented by Piet al (2017).</p> <p>Piet, GJ, HMJ van Overzee, DCM Miller, E Royo Gelabert, 2017. Indicators of the ‘wild seafood’ provisioning ecosystem service based on the surplus production of commercial fish stocks. Ecological Indicators, Volume 72: 194-202.</p>
"Out of South Asia": distinctive genomic profile of wild boar and domestic pig populations in South Asia
<p> content:</p> <p>hic matrix for p1, p2, p3</p>
Supplementary material from "Utilising citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry."
<p>Stephen H. Vickers, Jayna Raghwani, Ashley C. Banyard, Ian H. Brown, Guillaume Fournie and Sarah C. Hill </p>
The Great British Liverwort Hunt – collecting wild accessions for molecular biology research while engaging the public
<p>During the lockdowns of the COVID-19 pandemic, outreach activities of universities were significantly perturbed. The Sainsbury Laboratory Cambridge University (SLCU) outreach project for the Cambridge festival in 2021 was therefore a fully online project, which asked people from across the mainland of the United Kingdom to send in plant samples of <i>Marchantia polymorpha</i>, and <i>Lunularia cruciata. </i>The samples were, upon arrival, established into axenic culture for use in research. Here, we deposit the names and locational data of the lines established in axenic culture for the wider use of the research community. Out of 76 samples received, 68 were successfully established in sterile tissue culture. This dataset also includes an analysis of the sex of the <i>M. polymorpha</i> accessions.</p>
Fig. 1 in Species ofXystusSchönherr (Coleoptera: Curculionidae: Baridinae) are Seed Predators of Wild Yams (Dioscoreaceae) in Central Mexico
Fig. 1. Xystus gracilirostris on fruit capsule of Dioscorea sparsiflora. Oviposition puncture of weevil is present in lower right on fruit capsule.
Mapping firescapes for wild and prescribed fire management: a landscape classification approach
Open the record for dataset details and reuse information.
Data and code for: "Foraging rates from metabarcoding: Predators have reduced functional responses in wild, diverse prey communities."
<p>Data and code for "Foraging rates from metabarcoding: Predators have reduced functional responses in wild, diverse prey communities."</p>
Data and code for "Wild and captive immature orang-utans differ in their non-vocal communication with others, but not with their mothers"
Open the record for dataset details and reuse information.
Wagon3 from the Wild West
Wagon3 from the Wild West Source: Objaverse 1.0 / Sketchfab
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
<p><span>Microbiomes feature recurrent compositional structures under given environmental conditions. </span><span>However, these patterns may conceal diverse underlying population dynamics that require intra-strain resolution. Here, we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative PCR and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intra-strain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the <em>Arabidopsis</em> phyllosphere, both with and without microbiota context. We observed colonization resistance against late arriving strains of <em>Salmonella</em> typhimurium in the mouse gut, whereas the phyllosphere accommodated <em>Sphingomonas</em> latecomers in a proportional manner to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems. </span></p>
Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures
<p>Data files for Vogt et al. 2024</p>
Replication Package for Data Quality Assessment in the Wild: Findings from GitHub
<p>This contains the data and code used in the EASE 2014 paper "Data Quality Assessment in the Wild: Findings from GitHub."</p>
The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications
<div> <div> <p><a href="https://onlinelibrary.wiley.com/doi/10.1111/age.13181">https://onlinelibrary.wiley.com/doi/10.1111/age.13181</a></p> <h1>The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications</h1> <div> </div> <div> <div> <div> <div><a href="https://onlinelibrary.wiley.com/authored-by/Chen/Jianhai">Jianhai Chen</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Zhong/Jie">Jie Zhong</a>, <a href="https://onlinelibrary.wiley.com/authored-by/He/Xuefei">Xuefei He</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Li/Xiaoyu">Xiaoyu Li</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Ni/Pan">Pan Ni</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Safner/Toni">Toni Safner</a>, <a href="https://onlinelibrary.wiley.com/authored-by/%C5%A0prem/Nikica">Nikica Šprem</a>, <a href="https://onlinelibrary.wiley.com/authored-by/Han/Jianlin">Jianlin Han</a></div> </div> </div> </div> <p>The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long-range information provided by 10× Linked-Reads sequencing. We achieved a high-quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference-assistant scaffolding method. Using the ‘assembly-to-assembly’ approach, we identified intra-chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (<em>R</em><sup>2</sup> > 0.64, <em>p</em> < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large-scale inter-chromosomal evolution, by resolving parental-derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (<em>p</em> < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (<em>p</em> < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter-chromosomal interaction between the sex chromosome and autosomes.</p> </div> </div> <div>The work has been pulished here: https://onlinelibrary.wiley.com/doi/full/10.1111/age.13181</div> <div> </div> <div>The current dataset include the genome annotation files.</div> <div> </div> <div>For the whole-genomic assembly, please check NCBI: </div> <div>https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_021656055.1/</div> <div> <table> <tbody> <tr> <th> </th> <th>GenBank</th> </tr> </tbody> <tbody> <tr> <td>Genome size</td> <td>2.5 Gb</td> </tr> <tr> <td>Total ungapped length</td> <td>2.4 Gb</td> </tr> <tr> <td>Number of scaffolds</td> <td>12,642</td> </tr> <tr> <td>Scaffold N50</td> <td>28.3 Mb</td> </tr> <tr> <td>Scaffold L50</td> <td>25</td> </tr> <tr> <td>Number of contigs</td> <td>41,323</td> </tr> <tr> <td>Contig N50</td> <td>157.9 kb</td> </tr> <tr> <td>Contig L50</td> <td>4,562</td> </tr> <tr> <td>GC percent</td> <td>42</td> </tr> <tr> <td>Genome coverage</td> <td>56.0x</td> </tr> <tr> <td>Assembly level</td> <td>Scaffold</td> </tr> </tbody> </table> <p> </p> <h2>Assembly methods</h2> <div>Sequencing technology 10xgenomics Assembly method Supernova v. 2.1.1 <p> </p> <p>part_** are genome fasta for the GCA_021656055.1</p> <p>You could use the following to combine and uncompress.</p> </div> </div> <div> <div> <div><code><span>cat</span> part_* > archive_combined.zip </code></div> </div> <div> <div> </div> <div><code>unzip archive_combined.zip</code></div> </div> </div> <div> </div> <div> </div>
Pesticide risk during commercial apple pollination is greater for honeybees than other managed and wild bees
<p>Data and code relating to the manuscript “Pesticide risk during commercial apple pollination is greater for honeybees than other managed and wild bees”</p> <p>Files are organized as follows</p> <p><strong>input</strong> - contains the main data files.</p> <ul> <li> <p>all_pesticide2019.csv – contains the pesticide residue data for all samples</p> </li> <li> <p>LD50.csv – contains pesticide LD50s in PPB</p> </li> <li> <p>ld50_per_bee.csv – contains pesticide LD50s in ug / honeybee</p> </li> <li> <p>nesting_type.csv – lists nesting types of the different bee samples</p> </li> <li> <p>pesticide_type.csv – lists pesticides by their type</p> </li> <li> <p>short_name.csv – lists short bee names</p> <p><strong>folder “gis”</strong></p> <ul> <li>hive_distance_matrix.csv – distances from each orchard to other sites</li> <li>sitelocation.csv – contains coordinates of sites</li> </ul> </li> </ul> <p><strong>code</strong> - contains the scripts to analyze the input files</p> <ul> <li>pesticide_analysis.R – is the main anaylsis for the paper</li> <li>unadjusted_pesticide_analysis.R – is a copy of most of the code above but without LD50 weight adjustements</li> </ul> <p><strong>ld50 adjust</strong> - contains the inputs and code for the ld50 adjustments I ran</p> <ul> <li>ld50_adjust.R – is the code to calculate our the adjustements</li> <li>2020_BeeTox_database_acute_contact_publication_final_R1.csv – is the data file taken from pamminger publication</li> </ul>
RNA sequencing data from the prefrontal cortex and hippocampus of male (12 weeks old) hemizyguous CAG-HERV-W-env mice and wild-type controls
<p>RNA sequencing data from the prefrontal cortex (PFC) and hippocampus (HIPP) of male (12 weeks old) hemizyguous CAG<sup>HERV-Wenv </sup>mice ( C57BL6/J;129P2/Ola-Hprt mice; <em>n</em> = 3) relative to wild-type ( <em>n</em> = 3) littermates. Total RNA was extracted from prefrontal and hippocampal samples using the SPLIT RNA extraction kit (Lexogen, Austria) following the manufacturer’s recommendations and was sent to the Functional Genomics Center in Zurich (FGCZ) for quality control and RNA sequencing. The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1, a 28S/18S ratio within 1.5–2, and RIN (>8) values qualified for a Poly-A enrichment strategy in order to generate the sequencing libraries applying the TruSeq mRNA Stranded Library Prep Kit (Illumina, Inc, California, USA). After Poly-A selection using Oligo-dT beads the mRNA was reverse-transcribed into cDNA. The cDNA was fragmented, end-repaired and poly-adenylated before ligation of TruSeq UD Indices (IDT, Coralville, Iowa, USA). The quality and quantity of the amplified sequencing libraries were validated using a Fragment Analyzer SS NGS Fragment Kit (1–6000 bp) (Agilent, Waldbronn, Germany). The equimolar pool of the samples was spiked into a NovaSeq6000 run targeting ~15M reads per sample on a S1 FlowCell (Novaseq S1 Reagent Kit, 100 cycles, Illumina, Inc, California, USA). Reads were quality-checked with FastQC. Sequencing adapters were removed with Trimmomatic and aligned to the reference genome and transcriptome of Mus Musculus (GENCODE, GRCm38,p5) with STAR v2.7.3. Distribution of the reads across genomic isoform expression was quantified using the R package GenomicRanges from Bioconductor Version 3.10. Minimum mapping quality, as well as minimum feature overlaps, was set to 10. Multi-overlaps were allowed. Differentially expressed genes (DEGs) were identified using the R package edgeR from Bioconductor Version 3.10, using a generalized linear model (glm) regression, a quasi-likelihood (QL) differential expression test and the trimmed means of M-values (TMM) normalization.</p>
Figure 6 in Behavioral repertoire of a population of wild Chilean Flamingos Phoenicopterus chilensis in southern Brazil
Figure 6. Representations of agonistic social behaviours observed on Chilean Flamingos at Lagoa do Peixe National Park. a) Alert posture; b) Hooking or Threat posture 1; c) Neck swaying or Threat posture 2; d) Sparring or Fighting; e) Front pecking; f) Back pecking.
Figure 4 in Behavioral repertoire of a population of wild Chilean Flamingos Phoenicopterus chilensis in southern Brazil
Figure 4. Representations of locomotion behaviours observed on Chilean Flamingos at Lagoa do Peixe National Park. a) Walking; b) Strolling; c) Running; d) Flying.
Figure 3 in Behavioral repertoire of a population of wild Chilean Flamingos Phoenicopterus chilensis in southern Brazil
Figure 3. Representations of feeding behaviours observed on Chilean Flamingos at Lagoa do Peixe National Park. a) Pecking up; b) Head dipping; c) Feet trembling or Treading; d) Dredging or Moving Tread; e) False feet-trembling or false treading.
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.