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Fig. 2. Phylogenetic tree created using a in Dirofilaria immitis and Dirofilaria striata (Spirurida: Onchocercidae) detected in wild carnivores from Texas, United States
Fig. 2. Phylogenetic tree created using a maximum likelihood method (2000 bootstrap replicates) showing the relationship of identified Dirofilaria immitis and one isolate of Dirofilaria striata. Brugia pahangi sequence was used as outgroup.
Fig. 2 in Trypanosoma cruzi in domestic and wild mammals in the northeast region of Colombia
Fig. 2. Study area and detection of T. cruzi in domestic and wild mammals. Discrete typing units (DTUs): TcI (T cruzi I genotype), TcII (T cruzi II genotype), UK (unknown genotype).
Fig. 1 in Trypanosoma cruzi in domestic and wild mammals in the northeast region of Colombia
Fig. 1. Environmental characteristics of Villa Lucia village. a) Palms predominate in the vegetation; b) Crops and annexes adjacent to the house are present in the peridomicile.
Figure 1 in Domestication level of the most popular aquarium fish species: is the aquarium trade dependent on wild populations?
Figure 1. – Number of aquarium fish species per domestication level (white: freshwater, n = 50 species; black: marine, n = 50 species).
Fig. 2 in Pupal size distribution and sexual dimorphism in wild and laboratory populations of two species of Anastrepha (Diptera: Tephritidae) fruit flies
Fig. 2. Canonical analysis for pupae size parameters of males and females of laboratory and wild populations in Anastrepha ludens. The canonical analysis is represented on the first canonical axis (can 1), where the boxplots indicate the populations (laboratory and wild) and sexes (males and females) (lef). The variables of pupae size: length (mm), width (mm), and weight (mg) are indicated by vectors (right).
Fig. 1 in Pupal size distribution and sexual dimorphism in wild and laboratory populations of two species of Anastrepha (Diptera: Tephritidae) fruit flies
Fig. 1. Size distribution of laboratory and wild Anastrepha ludens and Anastrepha obliqua male and female pupae. The proportion of male and female pupae is shown in 10 pupal size classes (pupal diam mm) on the x-axis.
Fig. 3 in Pupal size distribution and sexual dimorphism in wild and laboratory populations of two species of Anastrepha (Diptera: Tephritidae) fruit flies
Fig. 3. Canonical analysis for pupae size parameters of males and females of laboratory and wild populations in Anastrepha obliqua. The canonical analysis is represented on the first canonical axis (can 1), where the boxplots indicate the populations (laboratory and wild) and sexes (males and females) (lef). The variables of pupae size: length (mm), width (mm), and weight (mg) are indicated by vectors (right).
Replication Package For An Extended Study of Syntactic Breaking Changes in the Wild
<p>This is the replication package associated with the paper titled 'An Extended Study of Syntactic Breaking Changes in the Wild' published under the Empirical Software Engineering journal.<br>Modern software applications rely heavily on the usage of libraries, which provide reusable functionality, to accelerate the development process. As libraries evolve and release new versions, the software systems that depend on those libraries (the clients) should update their dependencies to use these new versions as the new release could, for example, include critical fixes for security vulnerabilities. However, updating is not always a smooth process, as it can result in software failures in the clients if the new version<br>includes breaking changes. Yet, there is little research on how these breaking changes impact the client projects in the wild. <br>To identify if changes between two library versions cause breaking changes at the client end, we perform an empirical study on Java projects built using Maven. For the analysis, we used 18,415 Maven artifacts, which declared 142,355 direct dependencies, of which 71.60% were not up-to-date. We updated these dependencies and found<br>that 11.58% of the dependency updates contain breaking changes that impact the client. We further analyzed these changes in the library which impact the client projects and examine if libraries have adhered to the semantic versioning scheme when introducing breaking changes in their releases. Our results show that changes in transitive dependencies were a major factor in introducing breaking changes during dependency updates and almost half of the detected client impacting breaking changes violate the semantic versioning scheme by introducing breaking changes in non-Major upda</p>
Per-gene per-strain data: expression divergence between strains and alleles in F1s in wild C. elegans
<p>This dataset comprises p<span>er-gene per-strain data (used to perform all analyses and generate all figures), including regulatory pattern and inheritance mode classifications and underlying statistical differential expression results</span>.</p> <p>This is supplemental data for the linked preprint/publication describing insights derived from comparing gene expression (RNA-seq) between seven wild <em>C. elegans</em> strains and the laboratory reference strain N2, as well as the allelic expression of the wild and N2 alleles in F1s of crosses between all these wild strains and the reference strain.</p> <p>The PDF file <code>column_names_descriptions_worm_ase_data_pergene_perstrain.pdf</code> and excel spreadsheet <code>column_names_descriptions_worm_ase_data_pergene_perstrain.xlsx</code> serve as READMEs for the data file by providing details of the data held in each column of the data file <code>worm_ase_data_pergene_perstrain.txt.gz</code></p> <p>If you use this dataset (we hope someone does!), please cite the latest version of the accompanying preprint/publication.</p> <p>To query each gene in a user-friendly, visual format, see our shiny app <a href="https://wildworm.biosci.gatech.edu/ase/" target="_blank" rel="noopener">https://wildworm.biosci.gatech.edu/ase/</a></p>
Optimization of nuclei isolation for high-molecular weight DNA extraction of wild plants
<p><strong>Optimization of nuclei isolation for high-molecular weight DNA extraction from wild plants</strong></p> <p><strong>Authors</strong></p> <p>Irene Martínez-García<sup>1</sup>; Martina Degli Alberti<sup>2</sup>; Aureliano, Bombarely<sup>2</sup>; Mario Xavier Ruiz-González<sup>1</sup>; Santiago Vilanova<sup>1</sup>; Silvia Manrique<sup>1</sup></p> <p> </p> <p><strong>Affiliations</strong></p> <p>1 Instituto Universitario para la Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain) 2 Instituto de Biología Molecular y Celular de Plantas (IBMCP) Primo-Yufera, Consejo Superior de Investigaciones Científicas (CSIC)- Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain)</p> <p> </p> <p><strong>Abstract</strong></p> <p>Obtaining high-quality, high-molecular-weight (HMW) DNA is mandatory for constructing reference genomes, yet it remains a significant challenge, particularly for non-model plant species. Many plants contain polysaccharides and secondary metabolites such as polyphenols and tannins, which hinder DNA extraction. Exposure to multiple environmental stresses along their lives exacerbate this issue in wild plants collected from nature, as they may synthesize additional compounds that impair DNA extraction.</p> <p>This study investigates the efficacy of various DNA extraction protocols on four recalcitrant plant species—<em>Pistacia lentiscus</em>, <em>Phyllirea angustifolia</em>, <em>Sarcocornia fruticosa</em>, and <em>Limbarda crithmoides</em>—each possessing unique traits complicating DNA extraction (e.g., succulence, lignification, coloration). Samples were collected from El Saler (Valencia), and multiple protocols for nuclei isolation and DNA extraction were tested. The results were systematically evaluated to compile a comprehensive best practices guide, aiding researchers in selecting optimal methods tailored to their species of interest. This guide serves as a valuable resource for future endeavours in genome research, facilitating advancements in understanding and conservation efforts for diverse plant species.</p> <p>Funding: </p> <p>This work was supported by Erasmus+ Program (to MD), Programa María Zambrano 2021 (to SM and MXRG, UPV Ministerio de Universidades, Plan de Recuperación, Transformación y Resiliencia - Financiado por la Unión Europea – NextGenerationEU) and Catalan Initiative For the Earth Biogenome Project (Call1A-2023 to SM and call 2-2023 to AB and SM) and Primeros Proyectos UPV (PAID-06-22 to MXRG).</p>
Linked collectors and determiners for: Wild bees of Belgium.
Natural history specimen data linked to collectors and determiners held within, "Wild bees of Belgium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0d7c6a1a-0aab-47dc-8256-f23fefac69cd">https://bionomia.net/dataset/0d7c6a1a-0aab-47dc-8256-f23fefac69cd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0d7c6a1a-0aab-47dc-8256-f23fefac69cd">https://gbif.org/dataset/0d7c6a1a-0aab-47dc-8256-f23fefac69cd</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Eight new species of Andrena Fabricius (Hymenoptera: Apoidea: Andrenidae) from Israel — a Mediterranean hotspot for wild bees.
Natural history specimen data linked to collectors and determiners held within, "Eight new species of Andrena Fabricius (Hymenoptera: Apoidea: Andrenidae) from Israel — a Mediterranean hotspot for wild bees". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/49577e28-85f9-4cde-8e7f-3ec5baf7556f">https://bionomia.net/dataset/49577e28-85f9-4cde-8e7f-3ec5baf7556f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/49577e28-85f9-4cde-8e7f-3ec5baf7556f">https://gbif.org/dataset/49577e28-85f9-4cde-8e7f-3ec5baf7556f</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Resurveys of Wild Bee Communities (Apoidea: Anthophila) on The Dome in Pownal, Vermont, USA.
Natural history specimen data linked to collectors and determiners held within, "Resurveys of Wild Bee Communities (Apoidea: Anthophila) on The Dome in Pownal, Vermont, USA". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/bb574d56-86aa-41f7-b37f-a4259c94dd9c">https://bionomia.net/dataset/bb574d56-86aa-41f7-b37f-a4259c94dd9c</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bb574d56-86aa-41f7-b37f-a4259c94dd9c">https://gbif.org/dataset/bb574d56-86aa-41f7-b37f-a4259c94dd9c</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Flora of kurgans in the "Wild Fields" (Ukraine).
Natural history specimen data linked to collectors and determiners held within, "Flora of kurgans in the "Wild Fields" (Ukraine)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/59846cac-c4fd-4fde-bf45-5fe23d36f68f">https://bionomia.net/dataset/59846cac-c4fd-4fde-bf45-5fe23d36f68f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/59846cac-c4fd-4fde-bf45-5fe23d36f68f">https://gbif.org/dataset/59846cac-c4fd-4fde-bf45-5fe23d36f68f</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Vermont Wild Bee Survey (2019-2021).
Natural history specimen data linked to collectors and determiners held within, "Vermont Wild Bee Survey (2019-2021)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/6832470a-d8a2-4416-a302-7807295111c1">https://bionomia.net/dataset/6832470a-d8a2-4416-a302-7807295111c1</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6832470a-d8a2-4416-a302-7807295111c1">https://gbif.org/dataset/6832470a-d8a2-4416-a302-7807295111c1</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Wild bees of Grand Staircase-Escalante National Monument.
Natural history specimen data linked to collectors and determiners held within, "Wild bees of Grand Staircase-Escalante National Monument". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/491177c8-d074-46c0-9da3-0e9d1794936f">https://bionomia.net/dataset/491177c8-d074-46c0-9da3-0e9d1794936f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/491177c8-d074-46c0-9da3-0e9d1794936f">https://gbif.org/dataset/491177c8-d074-46c0-9da3-0e9d1794936f</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Updates to the checklist of the wild bee fauna of Luxembourg as inferred from revised natural history collection data and fieldwork.
Natural history specimen data linked to collectors and determiners held within, "Updates to the checklist of the wild bee fauna of Luxembourg as inferred from revised natural history collection data and fieldwork". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3f254e70-d5a0-4871-8c28-30a2004db17d">https://bionomia.net/dataset/3f254e70-d5a0-4871-8c28-30a2004db17d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3f254e70-d5a0-4871-8c28-30a2004db17d">https://gbif.org/dataset/3f254e70-d5a0-4871-8c28-30a2004db17d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Wild Bee Specimens from Blueberry and Raspberry Farms in the Champlain Valley, Vermont, USA.
Natural history specimen data linked to collectors and determiners held within, "Wild Bee Specimens from Blueberry and Raspberry Farms in the Champlain Valley, Vermont, USA". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/26c7440a-f4e4-4564-9901-9aac6e116536">https://bionomia.net/dataset/26c7440a-f4e4-4564-9901-9aac6e116536</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/26c7440a-f4e4-4564-9901-9aac6e116536">https://gbif.org/dataset/26c7440a-f4e4-4564-9901-9aac6e116536</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Wild bees of Chile - The PUCV collection.
Natural history specimen data linked to collectors and determiners held within, "Wild bees of Chile - The PUCV collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3bccb697-4ccc-4d46-848a-79cb06946e5c">https://bionomia.net/dataset/3bccb697-4ccc-4d46-848a-79cb06946e5c</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3bccb697-4ccc-4d46-848a-79cb06946e5c">https://gbif.org/dataset/3bccb697-4ccc-4d46-848a-79cb06946e5c</a>. Formatted as a Frictionless Data package.
Fig. 1.—A wild-caught adult male Lycalopex vetulus from 10 in Lycalopex vetulus (Carnivora: Canidae)
Fig. 1.—A wild-caught adult male Lycalopex vetulus from 10 km N Nova Xavantina, Mato Grosso State, Brazil. Photographed by author.
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.