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18,621 results for “development;”
Roadmap for Developing a Dynamic and Reproducible Research Article with ARTE workflow
<p>The figures illustrates a roadmap for developing a dynamic and reproducible research article using <strong>ARTE (Article Reproducibility Template & Environment) </strong>workflow. The process is categorized into three levels of reproducibility: <strong>Minimal, Proper, and Full</strong>. Each level integrates specific tools and practices to enhance the reproducibility of the research.</p> <p>This proposal is published in the following <strong>OSF project</strong>: <a title="OSF" href="https://osf.io/njdq5/" target="_blank" rel="noopener">https://osf.io/njdq5/</a><br>Shared in the following <strong>GitHub repository</strong>: <a title="GitHub" href="https://github.com/phdpablo/article-template" target="_blank" rel="noopener">https://github.com/phdpablo/article-template</a><br>Exemplified in the following <strong>URL address</strong>: <a title="Article Example" href="https://phdpablo.github.io/article-template/" target="_blank" rel="noopener">https://phdpablo.github.io/article-template/</a></p> <h1>Minimal Reproducibility</h1> <p><strong>1. Use this template</strong>: Start by utilizing the provided template, which is pre-configured with the <strong>TIER Protocol 4.0</strong>. This protocol helps organize research projects in a systematic manner.</p> <p><strong>2. Edit READMEs</strong>: Customize the README files to reflect the details and conclusions of your research. These README files help document the project structure and contents.</p> <p><strong>3. Share on OSF</strong>: Share the project on the <strong>Open Science Framework (OSF)</strong> to ensure accessibility and transparency. This can be done at the beginning, during, or at the end of the research process.</p> <h1>Proper Reproducibility</h1> <p>In addition to the steps mentioned above, the following steps are added:</p> <p><strong>4. Quarto settings:</strong> Adjust the Quarto configuration to fit the needs of your project. This includes modifying the <em>_quarto.yml</em> file for different themes and output formats.</p> <p><strong>5. Develop your narrative</strong>: Write the research narrative using <em>Quarto’s .qmd files</em> within RStudio. This narrative forms the main body of your article and integrates text, code, and outputs seamlessly.</p> <p><strong>6. Environment control:</strong> Implement environment control using the <em>renv package</em>. This ensures that the R environment is consistent and reproducible. The <em>renv.lock</em> file captures the exact versions of R packages used in the project.</p> <p><strong>7. Share dynamic article:</strong> Render and share the dynamic document via GitHub Pages. The Quarto-generated HTML files (docs folders) are hosted on GitHub Pages, making the research accessible and interactive.</p> <h1>Full Reproducibility</h1> <p>Building on the proper reproducibility steps, full reproducibility adds:</p> <p><strong>8. Use Docker:</strong> Employ Docker for operating system-level environment control. A Docker container encapsulates the entire project environment, ensuring that the research can be replicated exactly, regardless of the local machine setup.</p> <h2>Tools Utilized</h2> <ul> <li><strong>TIER Protocol 4.0</strong>: Provides a framework for organizing and documenting research projects.</li> <li><strong>OSF:</strong> A platform for sharing research outputs and ensuring open science practices.</li> <li><strong>Quarto:</strong> A tool for creating dynamic documents that integrate text, code, and outputs.</li> <li><strong>RStudio:</strong> An integrated development environment (IDE) for R, facilitating data analysis and reproducible research.</li> <li><strong>Git/GitHub:</strong> Version control systems that track changes and manage project versions.</li> <li><strong>renv: </strong>An R package for managing and reproducing consistent R environments.</li> <li><strong>GitHub Pages:</strong> A service for hosting static websites directly from a GitHub repository.</li> <li><strong>Docker:</strong> A platform for containerizing applications to ensure consistent environments across different systems.</li> </ul> <h2>Summary</h2> <p>This template guides researchers through creating a reproducible and dynamic article using ARTE (Article Reproducibility Template & Environment) workflow. It starts with basic project setup and documentation, progresses through developing the research narrative with environment control, and culminates in full reproducibility with Docker. This structured approach ensures that research is well-documented, versioned, and easily shareable, promoting open science practices.</p>
Dataset for project Lipobodies, related to the development of a new multicomponent process based on the combination of the isonitrile-tetrazine (4+1) cycloaddition and the Ugi four-component reaction
<p>This dataset contains primary (including raw data) that supports the results of the design and development of a new multicomponent process based on the combination of the isonitrile-tetrazine (4+1) cycloaddition and the Ugi four-component reaction</p>
Data from: Ontogeny of color development in two green-brown polymorphic grasshopper species
<p class="MsoNormal">Many insects, including several orthopterans, undergo dramatic changes in body coloration during ontogeny. This variation is particularly intriguing in gomphocerine grasshoppers, where the green and brown morphs appear to be genetically determined (Schielzeth & Dieker, 2020; Winter, Varma, & Schielzeth, 2021). A better understanding of how these color morphs develop during ontogeny can provide valuable insights into the evolution and ecology of such a widespread color polymorphism. Here, we focus on the color development of two green-brown polymorphic species, the club-legged grasshopper <em>Gomphocerus sibiricus </em>and the steppe grasshopper <em>Chorthippus</em> <em>dorsatus</em>. By following the color development of individuals from hatching to adulthood, we found that color morph differences begin to develop during the second nymphal stage,<span> are clearly defined by the third nymphal stage,</span> and remain stable throughout the life of an individual. Interestingly, we also observed that <span>shed skins of late nymphal stages are identifiable by color morphs based on their yellowish coloration, rather than the green that marks green body parts. </span>Furthermore, by assessing how these colors are perceived by different visual systems, we found that certain potential predators can chromatically discriminate between morphs, while others may not. These results suggest that the putative genes controlling color morph are active during the early stages of ontogeny, and that green color is likely composed of two components, one present in the cuticle and one not. In addition, the effectiveness of camouflage appears to vary depending on the specific predator involved.</p>
PRISMA-P (Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols) of the research entitled "Development of Competences for the Fashion Designer: a Scope Review
<p>PRISMA-P (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols) 2015 checklist: recommended items to address in a systematic review protocol and Check list CAPSI - Critical analysis of the articles related to the specific objective: map the current themes that permeate the competencies of fashion design professionals through a scoping review.</p>
Photosynthesis in newly-developed leaves of heat-tolerant wheat acclimates to long-term nocturnal warming
<p>We examined photosynthetic capacity of newly-developed and pre-existing flag leaves of four wheat genotypes under three night temperatures (15, 20 and 25 °C) and common day temperature of 26 °C in two controlled environment experiments. In newly-developed leaves which acclimated (i.e. maintained or increased) the maximum rate of net CO<sub>2</sub> assimilation (<em>A</em><sub>n</sub>) to long-term (9–13 weeks) nocturnal warming, acclimation was underpinned by greater capacity of Rubisco carboxylation (<em>V</em><sub>cmax</sub>) and photosynthetic electron transport (<em>J</em>). This indicates a night-dependent temperature sensitivity of the activation state of Rubisco. Metabolite profiling linked acclimation of <em>A</em><sub>n</sub> to greater accumulation of monosaccharides and saturated fatty acids in leaves, suggesting roles for osmotic adjustment of leaf turgor pressure and maintenance of cell membrane integrity. By contrast, warm night-induced inhibition of <em>A</em><sub>n</sub> was related to reductions in stomatal conductance of CO<sub>2</sub> and <em>J</em>, despite higher basal electron transport thermal stability: <em>T</em><sub>crit</sub> 51 of 45–46.5 °C in non-acclimated versus <em>T</em><sub>crit</sub> of 43.8–45 °C in acclimated leaves. Pre-existing leaves exposed to short-term nocturnal warming (5–7 nights) showed no change in instantaneous temperature responses of <em>A</em><sub>n</sub> and photosynthetic capacity, except for an elite heat-tolerant genotype. These findings can be used to support strategies for developing climate-resilient wheat.</p>
Fig.ç18.A mblyops surugensis sp. nov., holotype, female (NSMT-Cr 21364). A, rst thoracopodal endopod (le); B, second thoracopod (le); C, third thoracopod (le); D, distal part of endopod of the same limb (le); E, sixth thoracopod with rudimentary oostegite; F, eighth thoracopod with developed oostegite. in The Genus Amblyops (Crustacea: Mysida: Mysidae: Erythropinae) from East Asia and Australia, with Descriptions of Ten New Species
Fig.ç18.A mblyops surugensis sp. nov., holotype, female (NSMT-Cr 21364). A, rst thoracopodal endopod (le); B, second thoracopod (le); C, third thoracopod (le); D, distal part of endopod of the same limb (le); E, sixth thoracopod with rudimentary oostegite; F, eighth thoracopod with developed oostegite.
Fig.ç16.A mblyops sagamiensis sp. nov., A–E, I, allotype, male (NSMT-Cr 21362); F, H, holotype, female (NSMT-Cr 21361); G, J, paratype, female with partially developed marsupium (NSMT-Cr 21363). A, third pleopod (le); B, fourth pleopod (le); C, pseudobranchial lobe on the same limb (le); D, distal part of exopod of the same limb (le), E, h pleopod (right), F, G, uropod and telson (dorsal); H, I, proximal part of uropodal endopod (le, ventral); J, posterior part of telson (dorsal). in The Genus Amblyops (Crustacea: Mysida: Mysidae: Erythropinae) from East Asia and Australia, with Descriptions of Ten New Species
Fig.ç16.A mblyops sagamiensis sp. nov., A–E, I, allotype, male (NSMT-Cr 21362); F, H, holotype, female (NSMT-Cr 21361); G, J, paratype, female with partially developed marsupium (NSMT-Cr 21363). A, third pleopod (le); B, fourth pleopod (le); C, pseudobranchial lobe on the same limb (le); D, distal part of exopod of the same limb (le), E, h pleopod (right), F, G, uropod and telson (dorsal); H, I, proximal part of uropodal endopod (le, ventral); J, posterior part of telson (dorsal).
Fig.ç11.A mblyops paci cus sp. nov., immature female with partially developed marsupium (11.5 mm) (NSMT-Cr 21360). in The Genus Amblyops (Crustacea: Mysida: Mysidae: Erythropinae) from East Asia and Australia, with Descriptions of Ten New Species
Fig.ç11.A mblyops paci cus sp. nov., immature female with partially developed marsupium (11.5 mm) (NSMT-Cr 21360).
Figs. 117–122. 117. Ontholestes murinus, mesosternum with fully developed medial carina. 118 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 117–122. 117. Ontholestes murinus, mesosternum with fully developed medial carina. 118. Thoracostrongylus sp., mesosternum with short medial carina at base. 119. Dinothenarus fossor, labium with emarginate ligula, ventral view. 120. Dinothenarus pubescens, labium and mentum. 121. Dinothenarus pubescens, right mandible and right maxilla, ventral view. 122. Abemus chloropterus, mesosternum, showing sockets of serial setae originating behind small elevations.
FIGURES 23–28 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURES 23–28. Microphotographs of mature larvae of Euglossa (Euglossa) hemichlora. 23, 24. Right mandible, dorsal and inner views, respectively. 25. Anal area of cleared and stained predefecating larva with darkly stained integument above transverse anal slit above which is the pygidial ridge; dark area below slit is rectum seen through integument. Note short pigmented spines laterad of anal slit. 26. Spiracle of cleared predefecating larva seen from exterior, demonstrating width of peritreme relative to atrial opening. 27. Side view of spiracle of predefecating larva with its anatomical parts identified. 28. External view of spiracle of predefecating larva focused on unadorned primary tracheal opening; gray-toned ring immediately outside of opening caused by subatrium beneath transparent atrium.
FIGURES 15, 16 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURES 15, 16. SEM micrographs of egg of Euglossa (Euglossa) hemichlora. 15. Surface of chorion from side showing faint hexagonal patterning. 16. Presumed front end of egg revealing presumed opening through the vitelline membrane.
FIGURES 17–22 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURES 17–22. Diagrams of immature stages of Euglossa (Euglossa) hemichlora: figs. 18, 21, 22 to same scale. 17. Egg, presumed front end left. 18. Postdefecating larva, lateral view, anterior end left. 19, 20. Head of same, frontal and lateral views, respectively. 21. Late stage predefecating last larval instar, anterior end left. 22. Early stage of predefecating last larval instar, anterior end left.
FIGURES 11–14. Euglossine taxa not exhibiting elongate, necklike prothoracic segment. 11 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURES 11–14. Euglossine taxa not exhibiting elongate, necklike prothoracic segment. 11. Eulaema (Apeulaema) nigrita modified from Zucchi et al. (1969a: fig. 8) and 12, 13. Eufriesea surinamensis from Rozen (2016: figs. 6, 7) (both of which were identified as predefecating). 14. Exaerete smaragdina, identified as postdefecating in Garófalo and Rozen (2001: fig. 28), presumably was in an early stage that had not yet started to develop pupal tissue internally.
FIGURES 6–10 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURES 6–10. Euglossine taxa exhibiting elongate, necklike prothoracic segment and small cranium in Rozen (2016) for: 6, 7. Eufriesea surinamensis, 8. Eufriesea mussitans, 9. E. (Euglossa) cordata, 10. Eulaema (Apeulaema) polychroma.
FIGURES 3–5 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURES 3–5. Illustrations of sequence of immature stages of Euglossa (Glossura) intersecta Latreille reproduced from Zucchi et al. (1969b: figs. 3, 10, and 9, respectively), all to approximately same scale. 3. Postdefecating larva showing internal position of developing pharate pupa (dashed lines). 4. Prepupa. 5. Pupa, showing elongate mouthparts that form under the head and mesosoma of the prepupa.
FIGURE 1 in On Egg Eclosion and Larval Development in Euglossine Bees
FIGURE 1. Microphotographs of integument of body of cleared first instar of Eulaema (Apeulaema) nigrita (Lepeletier) showing two spiracles, associated trachea, and continuous band of fine spicules extending along one side of body just above spiracular line. Large structure circling each spiracle is large atrium of second instars forming around very small atrium or first instar. FIGURE 2. Close-up of one spiracle.
Figure 3 in Comparative ossification and development of the skull in palaeognathous birds (Aves: Palaeognathae)
Figure 3. Evolution of embryonic and adult palatal morphology of the ratites (phylogeny sensu Bledsoe, 1988, palaeognathous characters 1–3 sensu Zusi & Livezey, 2006). Top row: adult morphology (Parker, 1869, 1891; Beddard, 1898; Simonetta, 1960; Zusi & Livezey, 2006; Silveira & Höfling, 2007). Bottom row: embryonic morphology. Gallus (Jollie, 1957), Rhea, Apteryx (Parker, 1891), and Dromaius are all stage 37; Struthio (Parker, 1866) is slightly older; Aepyornis (Balanoff & Rowe, 2007) and Eudromia (Tinamidae) are late-stage individuals. The palatine is shaded to facilitate comparison.
Figure 2 in Comparative ossification and development of the skull in palaeognathous birds (Aves: Palaeognathae)
Figure 2. Palatal view of selected palaeognath embryos. A, B, Struthio camelus (modified from Parker, 1866). C, Rhea americana, stage 37 (day 17 of incubation, RM 7219). D, Rhea americana (modified from Müller, 1963). E, Dromaius novaehollandiae, stage 37 (day 28 of incubation, RM 8026). F, Eudromia elegans, day 14 of incubation (YPM 112524). Scale bars = 5 mm. Abbreviations: bo, basioccipital; exo, exoccipital; mx, maxilla; pal, palatine; pmx, premaxilla; psl, parasphenoid lamina; psr, parasphenoid rostrum; pt, pterygoid; q, quadrate; v, vomer.
Figs 1-4 in Nesting behaviour, male territoriality and larval development of Eremnophila binodis (F ) from Brazil (Hymenoptera: Sphecidae)
Figs 1-4: Laval development of a female Eremnophila binodis consuming a caterpillar. 1 Newly emerged larva; 2 larva immobile feeding the prey probably by sucking; 3 larva in the fourth day of development consuming externally the prey; 4 full-grown larva, the head capsule was the only portion of the prey that was not consumed.
Data for the publication "Developing a climatological simplification of aerosols to enter the cloud microphysics of a global climate model" - part 1
<p>The data is split into two datasets, for each to be smaller than 50 GB.</p>
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.