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51 results for “Material Engineering”
Not real or too soft? On the challenges of publishing interdisciplinary software engineering research (supplementary material)
<p>Supplementary material for paper "Not real or too soft? On the challenges of publishing interdisciplinary software engineering research" (ICSE 2025 SEIS track).</p>
Engineered Osteoclasts as Living Treatment Materials for Heterotopic Ossification Therapy
<p>All data generated in this study are provided in the Supplementary materials and raw data. The data that support the findings of this study are available from the corresponding authors in reasonable request.</p>
Supplementary material 1 from: Van De Walle R, Massol F, Vandegehuchte ML, Bonte D (2022) The distribution and impact of an invasive plant species (Senecio inaequidens) on a dune building engineer (Calamagrostis arenaria). NeoBiota 72: 1-23. https://doi.org/10.3897/neobiota.72.78511
Tables S1, S2, Figures S1, S2
Engineered Self-Organization for Resilient Robot Self-Assembly with Minimal Surprise - Paper Material
<p>Supplementary Videos </p>
What do LinkedIn Brazilian Ads ask of Requirements Engineers? - Supplementary Material
Open the record for dataset details and reuse information.
Supplementary material 1 from: Shaffer JA, Parks D, Campbell K, Moragne A, Hueske B, Adams P, Bauman JM (2023) Coastal beaver, Chinook, coho, chum salmon and trout response to nearshore changes resulting from diking and large-scale dam removals: synergistic ecosystem engineering and restoration in the coastal zone. Nature Conservation 53: 61-83. https://doi.org/10.3897/natureconservation.53.85421
Mean woody plant abundance surveyed from the riparian and shrub-emergent marsh vegetation
Supplementary Materials of the Tutorial: "Promotion of Open Science in Requirements Engineering: Leveraging the ORKG and ORKG Ask for FAIR Scientific Information"
<h1>Summary</h1> <p>This collection contains all the supplementary materials of the second tutorial titled "<a href="https://conf.researchr.org/details/RE-2025/RE-2025-tutorials/1/Promotion-of-Open-Science-in-Requirements-Engineering-Leveraging-the-ORKG-and-ORKG-A" target="_blank" rel="noopener">Promotion of Open Science in Requirements Engineering: Leveraging the ORKG and ORKG Ask for FAIR Scientific Information</a>", accepted at the <a href="https://conf.researchr.org/home/RE-2025" target="_blank" rel="noopener">33rd IEEE International Requirements Engineering Conference 2025</a>.</p> <p>The materials complement the tutorial sessions and provide participants with resources to enhance their understanding and application of open science principles in the field of Requirements Engineering (RE) by leveraging the <a href="https://orkg.org/" target="_blank" rel="noopener">Open Research Knowledge Graph (ORKG)</a> and <a href="https://ask.orkg.org/" target="_blank" rel="noopener">ORKG Ask</a> for FAIR scientific information. These materials contain all the presentation slides and exercise materials so that everyone can repeat the theoretical presentations independently and carry out the practical exercises themselves at any time.</p> <h1>Contents</h1> <h2>1. Slides - All slides used in the tutorial.</h2> <table> <tbody> <tr> <td><strong>Files</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>0. RE25 Tutorial - All Sessions.pdf</td> <td>The complete set of all slides used in the tutorial, which are also provided individually for each session of the tutorial.</td> </tr> <tr> <td>1. RE25 Tutorial - Welcome.pdf</td> <td>The welcome with an overview of the content of the tutorial.</td> </tr> <tr> <td>2. RE 25 Tutorial - Introduction to Open Science in RE.pdf</td> <td>The theoretical introduction to open science regarding its importance, benefits, and incentives for researchers themselves and the wider RE community.</td> </tr> <tr> <td>3. RE25 Tutorial - Introduction to ORKG and ORKG Ask.pdf</td> <td>The theoretical introduction to the Open Research Knowledge Graph (ORKG) and ORKG Ask.</td> </tr> <tr> <td>4. RE25 Tutorial - Using SciKGTeX.pdf</td> <td>The practical exercise, with detailed step-by-step instructions on how to use the LaTeX package <a href="https://github.com/Christof93/SciKGTeX" target="_blank" rel="noopener">SciKGTeX</a> to create a FAIR-annotated publication and import it into the ORKG.</td> </tr> <tr> <td>5. RE25 Tutorial - Using the ORKG.pdf</td> <td>The practical exercise, with detailed step-by-step instructions on how to use the <a href="https://orkg.org/" target="_blank" rel="noopener">ORKG </a>to describe publications regarding their scientific information and use these descriptions to create and publish an ORKG comparison.</td> </tr> <tr> <td>6. RE25 Tutorial - Using the ORKG Ask and ORKG CSV Import.pdf</td> <td>The practical exercise, with detailed step-by-step instructions on how to use <a href="https://ask.orkg.org/" target="_blank" rel="noopener">ORKG Ask</a> and the <a href="https://orkg.org/" target="_blank" rel="noopener">ORKG</a> CSV Import to describe publications regarding their scientific information and use these descriptions to create and publish an ORKG comparison.</td> </tr> <tr> <td>7. RE25 Tutorial - Reflection and Closing.pdf</td> <td>The summary, reflection, and closing of the tutorial with an outlook to the future of <a href="https://gitlab.com/TIBHannover/orkg/ExtracTable" target="_blank" rel="noopener">ExtracTable</a>.</td> </tr> </tbody> </table> <h2>2. Exercise Materials - All exercise materials used in the tutorial.</h2> <h3>2.1 SciKGTeX Materials</h3> <table> <tbody> <tr> <td><strong>Folder</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>SciKGTeX_Example</td> <td> <p>The folder contains an example publication and all required SciKGTeX files for annotating the scientific information.</p> <p>Files:</p> <ol> <li>example.tex : LaTeX file of the example publication.</li> <li>scikgtex.lua : Required LaTeX package file for using SciKGTeX.</li> <li>scikgtex.sty : Required LaTeX package file for using SciKGTeX.</li> <li>project.zip : Zip file containing all above files for uploading as a project in Overleaf.</li> </ol> <p><em>Remark:</em> SciKGTeX is constantly being further developed. For the latest version of the required files, please refer to the corresponding <a href="https://github.com/Christof93/SciKGTeX" target="_blank" rel="noopener">GitHub project</a>.</p> </td> </tr> <tr> <td>SciKGTeX_Solution</td> <td> <p>The folder contains an Overleaf project with the solution for a possible annotation of the example publication provided.</p> <p>Files:</p> <ol> <li>example.pdf : PDF with annotations embedded into the PDF's XMP metadata.</li> <li>example.tex : LaTeX file of the example publication with annotations.</li> <li>output.xmp_metadata.xml : XMP file generated by SciKGTeX to check the annotations created.</li> <li>scikgtex.lua : Required LaTeX package file for using SciKGTeX.</li> <li>scikgtex.sty : Required LaTeX package file for using SciKGTeX.</li> <li>project.zip : Zip file containing all above files for uploading as a project in Overleaf.</li> </ol> <p><em>Remark:</em> SciKGTeX is constantly being further developed. For the latest version of the required files, please refer to the corresponding <a href="https://github.com/Christof93/SciKGTeX" target="_blank" rel="noopener">GitHub project</a>.</p> </td> </tr> </tbody> </table> <h3>2.2 ORKG Materials</h3> <table> <tbody> <tr> <td><strong>Folder</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>ORKG_Exemplary_Comparison</td> <td> <p>The folder contains a created ORKG comparison as a PDF and PNG file, consisting of 4 exemplary publications that were described with the ORKG template provided for the tutorial.</p> </td> </tr> <tr> <td>ORKG_Exemplary_Publications</td> <td> <p>The folder contains 20 PDF files with short summaries of scientific findings on empirical research practices from 20 different publications of the IEEE International Requirements Engineering Conference. The participants have received these PDFs to enter them in the ORKG and then create an ORKG Comparison.</p> <p><em>Remark:</em> We have provided the short summaries instead of the full publications to simplify the extraction process due to time constraints.</p> </td> </tr> <tr> <td>ORKG_Template</td> <td> <p>The folder contains an overview of the ORKG template used in the tutorial as a PNG file and an N3 file of its RDF structure.</p> </td> </tr> </tbody> </table> <h3>2.3 ORKG Ask & ORKG CSV Import Materials</h3> <table> <tbody> <tr> <td><strong>File</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>empty_orkg_csv_file_for_orkg_csv_import.csv</td> <td> <p>The file contains an empty template for creating an ORKG CSV file for the ORKG CSV Import with own content.</p> </td> </tr> <tr> <td>empty_orkg_csv_file_for_orkg_csv_import.xlsx</td> <td> <p> </p> The file contains an empty template for creating an ORKG CSV file for the ORKG CSV Import with own content. <p> </p> </td> </tr> <tr> <td>orkg_ask_synthesized_answer_and_link_to search.txt</td> <td>The file contains the synthesized answer with references from ORKG Ask for the question "What is the state of the art in empirical research applied in requirements engineering?" with a link to the associated saved search.</td> </tr> <tr> <td>original_orkg_ask_export_for_orkg_csv_import.csv</td> <td> <p>The file contains the original content of an exported ORKG Ask result table that is revised in the tutorial to create an ORKG Comparison using the ORKG CSV Import.</p> </td> </tr> <tr> <td>original_orkg_ask_export_for_orkg_csv_import.xlsx</td> <td> <p>The file contains the original content of an exported ORKG Ask result table that is revised in the tutorial to create an ORKG Comparison using the ORKG CSV Import.</p> </td> </tr> <tr> <td>revised_orkg_ask_export_for_orkg_csv_import.csv</td> <td> <p>The file contains the revised content of an exported ORKG Ask result table that is used in the tutorial to create an ORKG Comparison using the ORKG CSV Import.</p> </td> </tr> <tr> <td>revised_orkg_ask_export_for_orkg_csv_import.xlsx</td> <td> <p>The file contains the revised content of an exported ORKG Ask result table that is used in the tutorial to create an ORKG Comparison using the ORKG CSV Import.</p> </td> </tr> </tbody> </table> <h1>Usage Notes</h1> <p>These materials are intended for use by the participants of the tutorial, the broader RE community, and everyone interested in open science. They are provided to support the long-term transition towards FAIR scientific information and to empower researchers to integrate open science infrastructures into their work.</p> <h1>License</h1> <p>The materials are released under <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank" rel="noopener">Creative Commons Attribution 4.0 International (CC BY 4.0) license</a>, allowing for reuse and distribution in accordance with open science practices.</p>
Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [RNA-seq]
GEO Series GSE269373. Mus musculus. 22 samples. Type: Expression profiling by high throughput sequencing.
Tissue-engineered oral epithelial barrier for dental material testing: towards establishing in vitro biomimetic models - Underlying data
<p>Underlying CT data of "<strong>Tissue-engineered oral epithelial barrier for dental material testing: towards establishing <em>in vitro </em>biomimetic models</strong>"<br><a href="https://doi.org/10.1089/ten.tec.2024.0154">https://doi.org/10.1089/ten.tec.2024.0154</a></p> <p>Foteini Machla a, Paraskevi Kyriaki Monou b, c, Chrysanthi Bekiari d, Dimitrios Andreadis e Evangelia Kofidou d, , Emmanouel Panteris f, Orestis L. Katsamenis g, h, Maria Kokoti a, Petros Koidis a, Imad About i, Dimitrios Fatourosb, c, Athina Bakopoulou a</p> <p>a Department of Prosthodontics, Tissue Engineering Core Unit, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>b Department of Pharmaceutical Technology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>c Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Thessaloniki 57001, Greece</p> <p>d Laboratory of Anatomy and Histology, Veterinary School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>e Department of Oral Medicine/Pathology, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>f Department of Botany, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>g μ-VIS X-ray Imaging Centre, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, United Kingdom</p> <p>h Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom UK</p> <p>i Centre National de la Recherche Scientifique, Institute of Movement Sciences, Aix Marseille University, Marseille 13385, France</p> <p> </p> <p><strong>Measurement of ΤΕΟΕ thickness</strong></p> <p>X-ray computed micro-tomography (μCT) as employed to examine the microstructure of the paraffin-embedded tissue engineered oral epithelium (TEOE), enabling comprehensive 3D assessment of thickness using volumetric analysis (cf. supplementary for imaging parameters) (11). Imaging was conducted using an isotropic voxel-edge of 6.0 μm. Local Thickness was carried out in 3D using the “Volume Thickness Map” tool within Dragonfly software (cf. supplementary), allowing for the visualization and quantification of the spatial distribution and variability of tissue thickness.</p> <p>Imaging was conducted at the University of Southampton’s μ-VIS X-ray Imaging Centre ( https://muvis.org ) / 3D X-ray Histology facility, utilizing a customised μCT scanner optimisedfor intricate histological analyses(1), based on Nikon’s XTH225ST system (Nikon Metrology, UK). Operating parameters were set at 80 kVp / 86 μA (6.88 W), with a source-to-object distance of 37.5 mm and a source-to-detector distance of 937.4 mm, resulting in a magnification factor of 25x and an isotropic voxel-edge of 6.0 μm. Imaging acquisition involved the collection of 4001 projections using a 2850 x 2850 dexels detector, by averaging 4 frames per projection, with an exposure time of 500 ms per projection.</p> <p>Visualisation and analysis of the reconstructed dataset was done using Dragonfly software (Comet Technologies Canada Inc.; software accessible at http://www.theobjects.com/dragonfly). Assessment of Local Thickness was carried out in 3D using the “Volume Thickness Map” tool within Dragonfly software, following segmentation of the tissue layer. Local thickness analysis allowed for the visualization and quantification of the spatial distribution and variability of thickness within the tissue engineered oral epithelium (TEOE).</p> <p>Visual representation of local thickness histograms was employed to elucidate the distribution of thickness throughout the TEOE. These histograms effectively illustrate the number of voxels associated with specific cross-sectional thickness, offering both a graphical depiction of the variation in thickness across the tissue sample, and a quantitative measure of the average thickness of the specimen.</p> <p>It's worth noting, the volumetric and non-destructive nature of the technique enabled whole-block imaging, which proved crucial in addressing challenges arising from tissue sample shrinkage. This shrinkage, a consequence of dehydration during the fixation process, can occur in some cases and lead led to the specimen wrapping. While wrapping is not a common occurrence, this analysis method allowed for the evaluation of challenging-shaped specimens, such as the wrapped one presented in Figure 4. Unlike conventional 2D methods such as classical histology, which rely on the angle of slicing and encounter limitations when dealing with non-perfectly perpendicular slicing, μCT-based XRH enables analysis of all specimens, including those with complex shapes.</p> <p> </p>
Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [snRNA-seq]
GEO Series GSE269381. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs
GEO Series GSE269404. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
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.